diff -Nru bppsuite-0.6.2/bppSuite/bppAlnScore.cpp bppsuite-0.7.0/bppSuite/bppAlnScore.cpp --- bppsuite-0.6.2/bppSuite/bppAlnScore.cpp 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/bppSuite/bppAlnScore.cpp 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,226 @@ +// +// File: bppAlnScore.cpp +// Created by: Julien Dutheil +// Created on: Dec Thu 15 16:16 2011 +// + +/* +Copyright or or Copr. Bio++ Development Team + +This software is a computer program whose purpose is to simulate sequence +data according to a phylogenetic tree and an evolutionary model. + +This software is governed by the CeCILL license under French law and +abiding by the rules of distribution of free software. You can use, +modify and/ or redistribute the software under the terms of the CeCILL +license as circulated by CEA, CNRS and INRIA at the following URL +"http://www.cecill.info". + +As a counterpart to the access to the source code and rights to copy, +modify and redistribute granted by the license, users are provided only +with a limited warranty and the software's author, the holder of the +economic rights, and the successive licensors have only limited +liability. + +In this respect, the user's attention is drawn to the risks associated +with loading, using, modifying and/or developing or reproducing the +software by the user in light of its specific status of free software, +that may mean that it is complicated to manipulate, and that also +therefore means that it is reserved for developers and experienced +professionals having in-depth computer knowledge. Users are therefore +encouraged to load and test the software's suitability as regards their +requirements in conditions enabling the security of their systems and/or +data to be ensured and, more generally, to use and operate it in the +same conditions as regards security. + +The fact that you are presently reading this means that you have had +knowledge of the CeCILL license and that you accept its terms. +*/ + +// From the STL: +#include +#include +#include + +using namespace std; + +#include +#include +#include + +// From SeqLib: +#include +#include +#include +#include +#include +#include + +using namespace bpp; + +void help() +{ + (*ApplicationTools::message << "__________________________________________________________________________").endLine(); + (*ApplicationTools::message << "bppalnscore parameter1_name=parameter1_value").endLine(); + (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); + (*ApplicationTools::message).endLine(); + (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); + (*ApplicationTools::message << "__________________________________________________________________________").endLine(); +} + +int main(int args, char** argv) +{ + cout << "******************************************************************" << endl; + cout << "* Bio++ Alignment Score, version 0.1 *" << endl; + cout << "* Author: J. Dutheil Last Modif. 15/12/11 *" << endl; + cout << "******************************************************************" << endl; + cout << endl; + + if (args == 1) + { + help(); + return 0; + } + + try { + + BppApplication bppalnscore(args, argv, "BppAlnScore"); + bppalnscore.startTimer(); + + // Get alphabet + Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppalnscore.getParams(), "", false, true, true); + + // Get the test alignment: + auto_ptr sitesTest(SequenceApplicationTools::getSiteContainer(alphabet, bppalnscore.getParams(), ".test", false, true)); + + // Get the reference alignment: + auto_ptr sitesRef(SequenceApplicationTools::getSiteContainer(alphabet, bppalnscore.getParams(), ".ref", false, true)); + + //We check if the two alignments are compatible: + vector namesTest = sitesTest->getSequencesNames(); + vector namesRef = sitesRef->getSequencesNames(); + if (namesTest != namesRef) { + ApplicationTools::displayTask("Reorder sequences in ref. alignment", true); + auto_ptr tmp(new AlignedSequenceContainer(sitesRef->getAlphabet())); + for (size_t i = 0; i < namesTest.size(); ++i) { + ApplicationTools::displayGauge(i, namesTest.size() - 1); + try { + tmp->addSequence(sitesRef->getSequence(namesTest[i])); + } catch(SequenceNotFoundException& ex) { + throw Exception("ERROR!!! Reference alignment should contain the same sequences as the test alignment!"); + } + } + ApplicationTools::displayTaskDone(); + sitesRef = tmp; + } + + //Build alignment indexes: + RowMatrix indexTest, indexRef; + SiteContainerTools::getSequencePositions(*sitesTest, indexTest); + SiteContainerTools::getSequencePositions(*sitesRef, indexRef); + + //Now build scores: + int na = ApplicationTools::getIntParameter("score.na", bppalnscore.getParams(), 0); + ApplicationTools::displayResult("NA value to used", na); + vector cs = SiteContainerTools::getColumnScores(indexTest, indexRef, na); + vector sps = SiteContainerTools::getSumOfPairsScores(indexTest, indexRef, static_cast(na)); + + //Should scores be averaged for words? + size_t wsize = ApplicationTools::getParameter("score.word_size", bppalnscore.getParams(), 1); + size_t phase = 0; + if (wsize > 1) { + ApplicationTools::displayResult("Scores uniformized for words of size", wsize); + string phaseOpt = ApplicationTools::getStringParameter("score.phase", bppalnscore.getParams(), "1"); + if (TextTools::isDecimalInteger(phaseOpt)) { + phase = TextTools::toInt(phaseOpt); + if (phase == 0) + throw Exception("ERROR: positions are 1-based."); + phase--; + } else { + //We look for the first occurrence of the given motif: + try { + BasicSequence motif("motif", phaseOpt, sitesTest->getAlphabet()); + ApplicationTools::displayResult("Phase based on 1st occurence of", motif.toString()); + unsigned int pos = sitesTest->getNumberOfSites(); + for (unsigned int i = 0; i < sitesTest->getNumberOfSequences(); ++i) { + unsigned int p = SequenceTools::findFirstOf(sitesTest->getSequence(i), motif); + if (p < pos) + pos = p; + } + phase = pos; + } catch(Exception& ex) { + throw Exception("Error, unvalid motif specified for phase option."); + } + } + ApplicationTools::displayResult("First word starts at", phase + 1); + + //Now perform the smoothing: + size_t i; + for (i = 0; i < phase; ++i) { + cs[i] = 0; + sps[i] = 0; + } + for (; i + wsize <= cs.size(); i += wsize) { + //First compute minimum criterion: + int csmin = 1; + double spsmin = 1; + for (size_t j = i; j < i + wsize; ++j) { + if (cs[j] < csmin) csmin = cs[j]; + if (sps[j] < spsmin) spsmin = sps[j]; + } + //Assign min to all positions in word: + for (size_t j = i; j < i + wsize; ++j) { + cs[j] = csmin; + sps[j] = spsmin; + } + } + for (; i < cs.size(); ++i) { + cs[i] = 0; + sps[i] = 0; + } + } + + //Output scores to file: + string outputScores = ApplicationTools::getAFilePath("output.scores", bppalnscore.getParams(), false, false); + if (outputScores != "none") { + ApplicationTools::displayResult("Output scores to", outputScores); + ofstream output(outputScores.c_str(), ios::out); + output << "Site\tColumnScore\tSumOfPairsScore" << endl; + for (size_t i = 0; i < cs.size(); ++i) { + output << sitesTest->getSite(i).getPosition() << "\t" << cs[i] << "\t" << sps[i] << endl; + } + output.close(); + } + + //Create a sequence filter: + string outputFilter = ApplicationTools::getAFilePath("output.mase", bppalnscore.getParams(), false, false); + if (outputFilter != "none") { + ApplicationTools::displayResult("Output mase with site filter to", outputFilter); + double spsThreshold = ApplicationTools::getDoubleParameter("output.sps_thresholds", bppalnscore.getParams(), 0.8); + ApplicationTools::displayResult("Threshold for SPS", spsThreshold); + + MultiRange csRanges; + MultiRange spsRanges; + for (size_t i = 0; i < cs.size(); ++i) { + if (cs[i] == 1) csRanges.addRange(Range(i, i + 1)); + if (sps[i] >= spsThreshold) spsRanges.addRange(Range(i, i + 1)); + } + + MaseHeader header; + header.setSiteSelection("CS", csRanges); + header.setSiteSelection("SPS", spsRanges); + Mase writer; + writer.writeMeta(outputFilter, *sitesTest, header); + } + + //We're done! + bppalnscore.done(); + + } catch(exception & e) { + cout << e.what() << endl; + return 1; + } + + return 0; +} + diff -Nru bppsuite-0.6.2/bppSuite/bppAncestor.cpp bppsuite-0.7.0/bppSuite/bppAncestor.cpp --- bppsuite-0.6.2/bppSuite/bppAncestor.cpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/bppSuite/bppAncestor.cpp 2012-02-15 22:04:28.000000000 +0000 @@ -90,9 +90,9 @@ int main(int args, char ** argv) { cout << "******************************************************************" << endl; - cout << "* Bio++ Ancestral Sequence Reconstruction, version 0.4.0 *" << endl; + cout << "* Bio++ Ancestral Sequence Reconstruction, version 0.5.0 *" << endl; cout << "* Authors: J. Dutheil Created on: 10/09/08 *" << endl; - cout << "* B. Boussau Last Modif: 09/11/10 *" << endl; + cout << "* B. Boussau Last Modif: 17/06/11 *" << endl; cout << "******************************************************************" << endl; cout << endl; @@ -271,109 +271,158 @@ AncestralStateReconstruction *asr = 0; bool probMethod = false; - if (reconstruction == "marginal") + if (reconstruction == "none") { + //do nothing + } else if (reconstruction == "marginal") { asr = new MarginalAncestralStateReconstruction(tl); probMethod = true; - } - else + } else throw Exception("Unknown ancestral state reconstruction method: " + reconstruction); - if (probMethod) - { - probs = ApplicationTools::getBooleanParameter("asr.probabilities", bppancestor.getParams(), false, "", true, false); - ApplicationTools::displayResult("Output probabilities", probs ? "yes" : "no"); - } - - // Write infos to file: - string outputFile = ApplicationTools::getAFilePath("output.sites.file", bppancestor.getParams(), false, false); - if (outputFile != "none") - { - ApplicationTools::displayResult("Output file for sites", outputFile); - ofstream out(outputFile.c_str(), ios::out); - TreeTemplate ttree(*tree); - vector nodes = ttree.getInnerNodes(); - unsigned int nbNodes = nodes.size(); + string outputFile; + if (asr) { + if (probMethod) + { + probs = ApplicationTools::getBooleanParameter("asr.probabilities", bppancestor.getParams(), false, "", true, false); + ApplicationTools::displayResult("Output probabilities", probs ? "yes" : "no"); + } + + // Write infos to file: + outputFile = ApplicationTools::getAFilePath("output.sites.file", bppancestor.getParams(), false, false); + if (outputFile != "none") + { + ApplicationTools::displayResult("Output file for sites", outputFile); + ofstream out(outputFile.c_str(), ios::out); + TreeTemplate ttree(*tree); + vector nodes = ttree.getInnerNodes(); + unsigned int nbNodes = nodes.size(); - // Get the rate class with maximum posterior probability: - vector classes = tl->getRateClassWithMaxPostProbOfEachSite(); - // Get the posterior rate, i.e. rate averaged over all posterior probabilities: - Vdouble rates = tl->getPosteriorRateOfEachSite(); - // Get the ancestral sequences: - vector sequences(nbNodes); - vector probabilities(nbNodes); + // Get the rate class with maximum posterior probability: + vector classes = tl->getRateClassWithMaxPostProbOfEachSite(); + // Get the posterior rate, i.e. rate averaged over all posterior probabilities: + Vdouble rates = tl->getPosteriorRateOfEachSite(); + // Get the ancestral sequences: + vector sequences(nbNodes); + vector probabilities(nbNodes); + + vector colNames; + colNames.push_back("Sites"); + colNames.push_back("is.complete"); + colNames.push_back("is.constant"); + colNames.push_back("lnL"); + colNames.push_back("rc"); + colNames.push_back("pr"); + for (unsigned int i = 0; i < nbNodes; i++) { + Node *node = nodes[i]; + colNames.push_back("max." + TextTools::toString(node->getId())); + if (probs) { + probabilities[i] = new VVdouble(); + //The cast will have to be updated when more probabilistic method will be available: + sequences[i] = dynamic_cast(asr)->getAncestralSequenceForNode(node->getId(), probabilities[i], false); - vector colNames; - colNames.push_back("Sites"); - colNames.push_back("is.complete"); - colNames.push_back("is.constant"); - colNames.push_back("lnL"); - colNames.push_back("rc"); - colNames.push_back("pr"); - for (unsigned int i = 0; i < nbNodes; i++) { - Node *node = nodes[i]; - colNames.push_back("max." + TextTools::toString(node->getId())); - if (probs) { - probabilities[i] = new VVdouble(); - //The cast will have to be updated when more probabilistic method will be available: - sequences[i] = dynamic_cast(asr)->getAncestralSequenceForNode(node->getId(), probabilities[i], false); + for (unsigned int j = 0; j < nbStates; j++) { + colNames.push_back("prob." + TextTools::toString(node->getId()) + "." + alphabet->intToChar((int)j)); + } + } + else + { + if (node->isLeaf()) { - for (unsigned int j = 0; j < nbStates; j++) { - colNames.push_back("prob." + TextTools::toString(node->getId()) + "." + alphabet->intToChar((int)j)); + } else { + sequences[i] = asr->getAncestralSequenceForNode(node->getId()); + } } } - else - { - if (node->isLeaf()) { - } else { - sequences[i] = asr->getAncestralSequenceForNode(node->getId()); + //Now fill the table: + vector row(colNames.size()); + DataTable* infos = new DataTable(colNames); + + for (unsigned int i = 0; i < sites->getNumberOfSites(); i++) + { + double lnL = tl->getLogLikelihoodForASite(i); + const Site* currentSite = &sites->getSite(i); + int currentSitePosition = currentSite->getPosition(); + string isCompl = "NA"; + string isConst = "NA"; + try { isCompl = (SiteTools::isComplete(*currentSite) ? "1" : "0"); } + catch(EmptySiteException& ex) {} + try { isConst = (SiteTools::isConstant(*currentSite) ? "1" : "0"); } + catch(EmptySiteException& ex) {} + row[0] = (string("[" + TextTools::toString(currentSitePosition) + "]")); + row[1] = isCompl; + row[2] = isConst; + row[3] = TextTools::toString(lnL); + row[4] = TextTools::toString(classes[i]); + row[5] = TextTools::toString(rates[i]); + + unsigned int k = 6; + for (unsigned int j = 0; j < nbNodes; j++) { + row[k] = sequences[j]->getChar(i); + k++; + if (probs) { + for (unsigned int l = 0; l < nbStates; l++) { + row[k] = TextTools::toString((*probabilities[j])[i][l]); + k++; + } + } } + + infos->addRow(row); } + + DataTable::write(*infos, out, "\t"); + + delete infos; } - //Now fill the table: - vector row(colNames.size()); - DataTable* infos = new DataTable(colNames); - - for (unsigned int i = 0; i < sites->getNumberOfSites(); i++) + SiteContainer* asSites = 0; + if (probMethod) { - double lnL = tl->getLogLikelihoodForASite(i); - const Site* currentSite = &sites->getSite(i); - int currentSitePosition = currentSite->getPosition(); - string isCompl = "NA"; - string isConst = "NA"; - try { isCompl = (SiteTools::isComplete(*currentSite) ? "1" : "0"); } - catch(EmptySiteException& ex) {} - try { isConst = (SiteTools::isConstant(*currentSite) ? "1" : "0"); } - catch(EmptySiteException& ex) {} - row[0] = (string("[" + TextTools::toString(currentSitePosition) + "]")); - row[1] = isCompl; - row[2] = isConst; - row[3] = TextTools::toString(lnL); - row[4] = TextTools::toString(classes[i]); - row[5] = TextTools::toString(rates[i]); - - unsigned int k = 6; - for (unsigned int j = 0; j < nbNodes; j++) { - row[k] = sequences[j]->getChar(i); - k++; - if (probs) { - for (unsigned int l = 0; l < nbStates; l++) { - row[k] = TextTools::toString((*probabilities[j])[i][l]); - k++; - } + bool sample = ApplicationTools::getBooleanParameter("asr.sample", bppancestor.getParams(), false, "", true, false); + ApplicationTools::displayResult("Sample from posterior distribution", sample ? "yes" : "no"); + if (sample) + { + unsigned int nbSamples = ApplicationTools::getParameter("asr.sample.number", bppancestor.getParams(), 1, "", true, false); + asSites = new AlignedSequenceContainer(alphabet); + for (unsigned int i = 0; i < nbSamples; i++) + { + ApplicationTools::displayGauge(i, nbSamples-1, '='); + SequenceContainer *sampleSites = dynamic_cast(asr)->getAncestralSequences(true); + vector names = sampleSites->getSequencesNames(); + for (unsigned int j = 0; j < names.size(); j++) + names[j] += "_" + TextTools::toString(i+1); + sampleSites->setSequencesNames(names, false); + SequenceContainerTools::append(*asSites, *sampleSites); + delete sampleSites; } + ApplicationTools::message->endLine(); } - - infos->addRow(row); + else + { + asSites = asr->getAncestralSequences(); + } + } + else + { + asSites = asr->getAncestralSequences(); + } + + //Add existing sequence to output? + bool addExtant = ApplicationTools::getBooleanParameter("asr.add_extant", bppancestor.getParams(), false, "", true, false); + if (addExtant) { + SequenceContainerTools::append(*asSites, *sites); } - DataTable::write(*infos, out, "\t"); + //Write output: + if (ApplicationTools::getStringParameter("output.sequence.file", bppancestor.getParams(), "none") != "none") { + SequenceApplicationTools::writeAlignmentFile(*asSites, bppancestor.getParams()); + } + delete asSites; - delete infos; + delete asr; } - outputFile = ApplicationTools::getAFilePath("output.nodes.file", bppancestor.getParams(), false, false); if (outputFile != "none") @@ -381,15 +430,18 @@ ApplicationTools::displayResult("Output file for nodes", outputFile); ofstream out(outputFile.c_str(), ios::out); + //Add existing sequence to output? + bool addExtant = ApplicationTools::getBooleanParameter("output.nodes.add_extant", bppancestor.getParams(), false, "", true, false); + map > frequencies; - TreeLikelihoodTools::getAncestralFrequencies(*tl, frequencies, false); + TreeLikelihoodTools::getAncestralFrequencies(*tl, frequencies, addExtant); vector colNames; colNames.push_back("Nodes"); for (unsigned int i = 0; i < tl->getNumberOfStates(); i++) - colNames.push_back("exp" + TextTools::toString(i)); + colNames.push_back("exp" + alphabet->intToChar(i)); for (unsigned int i = 0; i < tl->getNumberOfStates(); i++) - colNames.push_back("eb" + TextTools::toString(i)); + colNames.push_back("eb" + alphabet->intToChar(i)); //Now fill the table: vector row(colNames.size()); @@ -416,50 +468,6 @@ } - - SiteContainer* asSites = 0; - if (probMethod) - { - bool sample = ApplicationTools::getBooleanParameter("asr.sample", bppancestor.getParams(), false, "", true, false); - ApplicationTools::displayResult("Sample from posterior distribution", sample ? "yes" : "no"); - if (sample) - { - unsigned int nbSamples = ApplicationTools::getParameter("asr.sample.number", bppancestor.getParams(), 1, "", true, false); - asSites = new AlignedSequenceContainer(alphabet); - for (unsigned int i = 0; i < nbSamples; i++) - { - ApplicationTools::displayGauge(i, nbSamples-1, '='); - SequenceContainer *sampleSites = dynamic_cast(asr)->getAncestralSequences(true); - vector names = sampleSites->getSequencesNames(); - for (unsigned int j = 0; j < names.size(); j++) - names[j] += "_" + TextTools::toString(i+1); - sampleSites->setSequencesNames(names, false); - SequenceContainerTools::append(*asSites, *sampleSites); - delete sampleSites; - } - ApplicationTools::message->endLine(); - } - else - { - asSites = asr->getAncestralSequences(); - } - } - else - { - asSites = asr->getAncestralSequences(); - } - - //Add existing sequence to output? - bool addExtant = ApplicationTools::getBooleanParameter("asr.add_extant", bppancestor.getParams(), false, "", true, false); - if (addExtant) { - SequenceContainerTools::append(*asSites, *sites); - } - - //Write output: - SequenceApplicationTools::writeAlignmentFile(*asSites, bppancestor.getParams()); - delete asSites; - - delete asr; delete alphabet; delete sites; if(model) delete model; diff -Nru bppsuite-0.6.2/bppSuite/bppML.cpp bppsuite-0.7.0/bppSuite/bppML.cpp --- bppsuite-0.6.2/bppSuite/bppML.cpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/bppSuite/bppML.cpp 2012-02-15 22:04:28.000000000 +0000 @@ -216,8 +216,6 @@ } DiscreteRatesAcrossSitesTreeLikelihood* tl; - string optimizeClock = ApplicationTools::getStringParameter("optimization.clock", bppml.getParams(), "no", "", true, false); - ApplicationTools::displayResult("Clock", optimizeClock); string nhOpt = ApplicationTools::getStringParameter("nonhomogeneous", bppml.getParams(), "no", "", true, false); ApplicationTools::displayResult("Heterogeneous model", nhOpt); @@ -228,8 +226,10 @@ SubstitutionModelSet* modelSet = 0; DiscreteDistribution* rDist = 0; - if (optimizeClock == "global") + if (optimizeTopo || nbBS > 0) { + if (nhOpt != "no") + throw Exception("Topology estimation with NH model not supported yet, sorry :("); model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, sites, bppml.getParams()); if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) @@ -242,164 +242,140 @@ rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); } if (dynamic_cast(model) == 0) - tl = new RHomogeneousClockTreeLikelihood(*tree, *sites, model, rDist, true, true); + tl = new NNIHomogeneousTreeLikelihood(*tree, *sites, model, rDist, true, true); else - throw Exception("Molecular clock with Mixed model not supported yet, sorry :("); + throw Exception("Topology estimation with Mixed model not supported yet, sorry :("); } - else if (optimizeClock == "no") + else if (nhOpt == "no") { - if (optimizeTopo || nbBS > 0) + model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, sites, bppml.getParams()); + if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); + if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) { - if (nhOpt != "no") - throw Exception("Topology estimation with NH model not supported yet, sorry :("); - model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, sites, bppml.getParams()); - if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); - if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) - { - // Markov-modulated Markov model! - rDist = new ConstantDistribution(1., true); - } - else - { - rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); - } - if (dynamic_cast(model) == 0) - tl = new NNIHomogeneousTreeLikelihood(*tree, *sites, model, rDist, true, true); - else - throw Exception("Topology estimation with Mixed model not supported yet, sorry :("); + // Markov-modulated Markov model! + rDist = new ConstantDistribution(1., true); } - else if (nhOpt == "no") + else { - model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, sites, bppml.getParams()); - if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); - if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) - { - // Markov-modulated Markov model! - rDist = new ConstantDistribution(1., true); - } - else - { - rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); - } - string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, false); - ApplicationTools::displayResult("Likelihood recursion", recursion); - if (recursion == "simple") - { - string compression = ApplicationTools::getStringParameter("likelihood.recursion_simple.compression", bppml.getParams(), "recursive", "", true, false); - ApplicationTools::displayResult("Likelihood data compression", compression); - if (compression == "simple") - if (dynamic_cast(model) == 0) - tl = new RHomogeneousTreeLikelihood(*tree, *sites, model, rDist, true, true, false); - else - tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true, true, false); - - else if (compression == "recursive") - if (dynamic_cast(model) == 0) - tl = new RHomogeneousTreeLikelihood(*tree, *sites, model, rDist, true, true, true); - else - tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true, true, true); + rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); + } + string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, false); + ApplicationTools::displayResult("Likelihood recursion", recursion); + if (recursion == "simple") + { + string compression = ApplicationTools::getStringParameter("likelihood.recursion_simple.compression", bppml.getParams(), "recursive", "", true, false); + ApplicationTools::displayResult("Likelihood data compression", compression); + if (compression == "simple") + if (dynamic_cast(model) == 0) + tl = new RHomogeneousTreeLikelihood(*tree, *sites, model, rDist, false, true, false); + else + tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, false, true, false); - else throw Exception("Unknown likelihood data compression method: " + compression); - } - else if (recursion == "double") - { + else if (compression == "recursive") if (dynamic_cast(model) == 0) - tl = new DRHomogeneousTreeLikelihood(*tree, *sites, model, rDist, true); + tl = new RHomogeneousTreeLikelihood(*tree, *sites, model, rDist, false, true, true); else - tl = new DRHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true); - } - else throw Exception("Unknown recursion option: " + recursion); + tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, false, true, true); + + else throw Exception("Unknown likelihood data compression method: " + compression); } - else if (nhOpt == "one_per_branch") + else if (recursion == "double") { - model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, sites, bppml.getParams()); - if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); - if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) - { - // Markov-modulated Markov model! - rDist = new ConstantDistribution(1., true); - } + if (dynamic_cast(model) == 0) + tl = new DRHomogeneousTreeLikelihood(*tree, *sites, model, rDist, true); else - { - rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); - } - vector rateFreqs; - if (model->getNumberOfStates() != alphabet->getSize()) - { - // Markov-Modulated Markov Model... - unsigned int n = (unsigned int)(model->getNumberOfStates() / alphabet->getSize()); - rateFreqs = vector(n, 1. / (double)n); // Equal rates assumed for now, may be changed later (actually, in the most general case, - // we should assume a rate distribution for the root also!!! - } + tl = new DRHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true); + } + else throw Exception("Unknown recursion option: " + recursion); + } + else if (nhOpt == "one_per_branch") + { + model = PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, sites, bppml.getParams()); + if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); + if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) + { + // Markov-modulated Markov model! + rDist = new ConstantDistribution(1., true); + } + else + { + rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); + } + vector rateFreqs; + if (model->getNumberOfStates() != alphabet->getSize()) + { + // Markov-Modulated Markov Model... + unsigned int n = (unsigned int)(model->getNumberOfStates() / alphabet->getSize()); + rateFreqs = vector(n, 1. / static_cast(n)); // Equal rates assumed for now, may be changed later (actually, in the most general case, + // we should assume a rate distribution for the root also!!! + } - bool stationarity = ApplicationTools::getBooleanParameter("nonhomogeneous.stationarity", bppml.getParams(), false, "", false, false); - FrequenciesSet* rootFreqs = 0; - if (!stationarity) - { - rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, sites, bppml.getParams(), rateFreqs); - stationarity = !rootFreqs; - } - ApplicationTools::displayBooleanResult("Stationarity assumed", stationarity); + bool stationarity = ApplicationTools::getBooleanParameter("nonhomogeneous.stationarity", bppml.getParams(), false, "", false, false); + FrequenciesSet* rootFreqs = 0; + if (!stationarity) + { + rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, sites, bppml.getParams(), rateFreqs); + stationarity = !rootFreqs; + } + ApplicationTools::displayBooleanResult("Stationarity assumed", stationarity); - vector globalParameters = ApplicationTools::getVectorParameter("nonhomogeneous_one_per_branch.shared_parameters", bppml.getParams(), ',', ""); - for (unsigned int i = 0; i < globalParameters.size(); i++) - ApplicationTools::displayResult("Global parameter", globalParameters[i]); - modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, globalParameters); - model = 0; - - string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, false); - ApplicationTools::displayResult("Likelihood recursion", recursion); - if (recursion == "simple") - { - if (modelSet->hasMixedSubstitutionModel()) - tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); - else - tl = new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); - } - else if (recursion == "double") - { - if (modelSet->hasMixedSubstitutionModel()) - throw Exception("Double recursion with non homogeneous mixed models is not implemented yet."); - // tl = new DRNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); - else - tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); - } - else throw Exception("Unknown recursion option: " + recursion); + vector globalParameters = ApplicationTools::getVectorParameter("nonhomogeneous_one_per_branch.shared_parameters", bppml.getParams(), ',', ""); + for (unsigned int i = 0; i < globalParameters.size(); i++) + ApplicationTools::displayResult("Global parameter", globalParameters[i]); + modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, globalParameters); + model = 0; + + string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, false); + ApplicationTools::displayResult("Likelihood recursion", recursion); + if (recursion == "simple") + { + if (dynamic_cast(modelSet)!=NULL) + tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, dynamic_cast(modelSet), rDist, true, true); + else + tl = new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); } - else if (nhOpt == "general") + else if (recursion == "double") { - modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, sites, bppml.getParams()); - if (modelSet->getModel(0)->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); - if (modelSet->getNumberOfStates() >= 2 * modelSet->getAlphabet()->getSize()) - { - // Markov-modulated Markov model! - rDist = new ConstantDistribution(1., true); - } + if (dynamic_cast(modelSet)!=NULL) + throw Exception("Double recursion with non homogeneous mixed models is not implemented yet."); + // tl = new DRNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); else - { - rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); - } + tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); + } + else throw Exception("Unknown recursion option: " + recursion); + } + else if (nhOpt == "general") + { + modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, sites, bppml.getParams()); + if (modelSet->getModel(0)->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); + if (modelSet->getNumberOfStates() >= 2 * modelSet->getAlphabet()->getSize()) + { + // Markov-modulated Markov model! + rDist = new ConstantDistribution(1., true); + } + else + { + rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); + } - string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, false); - ApplicationTools::displayResult("Likelihood recursion", recursion); - if (recursion == "simple") - { - if (modelSet->hasMixedSubstitutionModel()) - tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); - else - tl = new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); - } - else if (recursion == "double") - if (modelSet->hasMixedSubstitutionModel()) - throw Exception("Double recursion with non homogeneous mixed models is not implemented yet."); - // tl = new DRNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); - else - tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); - else throw Exception("Unknown recursion option: " + recursion); + string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, false); + ApplicationTools::displayResult("Likelihood recursion", recursion); + if (recursion == "simple") + { + if (dynamic_cast(modelSet)!=NULL) + tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, dynamic_cast(modelSet), rDist, true, true); + else + tl = new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); } - else throw Exception("Unknown option for nonhomogeneous: " + nhOpt); + else if (recursion == "double") + if (dynamic_cast(modelSet)) + throw Exception("Double recursion with non homogeneous mixed models is not implemented yet."); + // tl = new DRNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); + else + tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); + else throw Exception("Unknown recursion option: " + recursion); } - else throw Exception("Unknown option for optimization.clock: " + optimizeClock); + else throw Exception("Unknown option for nonhomogeneous: " + nhOpt); tl->initialize(); @@ -487,16 +463,8 @@ } } - if (optimizeClock == "global") - { - PhylogeneticsApplicationTools::optimizeParameters( - dynamic_cast(tl), tl->getParameters(), bppml.getParams()); - } - else - { - tl = dynamic_cast( - PhylogeneticsApplicationTools::optimizeParameters(tl, tl->getParameters(), bppml.getParams())); - } + tl = dynamic_cast( + PhylogeneticsApplicationTools::optimizeParameters(tl, tl->getParameters(), bppml.getParams())); tree = new TreeTemplate(tl->getTree()); PhylogeneticsApplicationTools::writeTree(*tree, bppml.getParams()); @@ -526,6 +494,9 @@ out << "# Log likelihood = "; out.setPrecision(20) << (-tl->getValue()); out.endLine(); + out << "# Number of sites = "; + out.setPrecision(20) << sites->getNumberOfSites(); + out.endLine(); out.endLine(); out << "# Substitution model parameters:"; out.endLine(); @@ -601,11 +572,12 @@ // Bootstrap: - if (nbBS > 0 && optimizeClock != "no") + string optimizeClock = ApplicationTools::getStringParameter("optimization.clock", bppml.getParams(), "None", "", true, false); + if (nbBS > 0 && optimizeClock != "None") { ApplicationTools::displayError("Bootstrap is not supported with clock trees."); } - if (nbBS > 0 && optimizeClock == "no") + if (nbBS > 0 && optimizeClock == "None") { ApplicationTools::displayResult("Number of bootstrap samples", TextTools::toString(nbBS)); bool approx = ApplicationTools::getBooleanParameter("bootstrap.approximate", bppml.getParams(), true); diff -Nru bppsuite-0.6.2/bppSuite/bppSeqMan.cpp bppsuite-0.7.0/bppSuite/bppSeqMan.cpp --- bppsuite-0.6.2/bppSuite/bppSeqMan.cpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/bppSuite/bppSeqMan.cpp 2012-02-15 22:04:28.000000000 +0000 @@ -5,7 +5,7 @@ // /* -Copyright or or Copr. CNRS +Copyright or or Copr. Bio++ Development Team This software is a computer program whose purpose is to simulate sequence data according to a phylogenetic tree and an evolutionary model. @@ -59,6 +59,10 @@ #include #include +//From PhylLib: +#include +#include + using namespace bpp; void help() @@ -74,8 +78,8 @@ int main(int args, char** argv) { cout << "******************************************************************" << endl; - cout << "* Bio++ Sequence Manipulator, version 0.4 *" << endl; - cout << "* Author: J. Dutheil Last Modif. 07/02/11 *" << endl; + cout << "* Bio++ Sequence Manipulator, version 0.6 *" << endl; + cout << "* Author: J. Dutheil Last Modif. 21/12/11 *" << endl; cout << "******************************************************************" << endl; cout << endl; @@ -197,15 +201,15 @@ // +-------------+ else if (cmdName == "Translate") { - if (!AlphabetTools::isNucleicAlphabet(sequences->getAlphabet())) - throw Exception("Error in translation: alphabet is not of type 'nucleic'."); + if (!AlphabetTools::isCodonAlphabet(sequences->getAlphabet())) + throw Exception("Error in translation: alphabet is not of type 'codon'."); GeneticCode* gc = NULL; string gcstr = ApplicationTools::getStringParameter("code", cmdArgs, "Standard"); - gc = SequenceApplicationTools::getGeneticCode(dynamic_cast(sequences->getAlphabet()), gcstr); + gc = SequenceApplicationTools::getGeneticCode(dynamic_cast(sequences->getAlphabet())->getNucleicAlphabet(), gcstr); OrderedSequenceContainer* sc = 0; - if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); - else sc = reinterpret_cast(new VectorSequenceContainer(sequences->getAlphabet())); + if (aligned) sc = new VectorSiteContainer(&AlphabetTools::PROTEIN_ALPHABET); + else sc = reinterpret_cast(new VectorSequenceContainer(&AlphabetTools::PROTEIN_ALPHABET)); for (unsigned int i = 0; i < sequences->getNumberOfSequences(); i++) { Sequence* seq = gc->translate(sequences->getSequence(i)); @@ -223,9 +227,9 @@ VectorSequenceContainer* sc = new VectorSequenceContainer(sequences->getAlphabet()); for (unsigned int i = 0; i < sequences->getNumberOfSequences(); i++) { - Sequence* seq = SequenceTools::removeGaps(sequences->getSequence(i)); + auto_ptr seq(sequences->getSequence(i).clone()); + SequenceTools::removeGaps(*seq); sc->addSequence(*seq); - delete seq; } delete sequences; sequences = sc; @@ -273,10 +277,40 @@ // +--------------+ else if (cmdName == "RemoveStops") { - SiteContainer* sites = dynamic_cast(sequences); + SiteContainer* sites = dynamic_cast(sequences); + if (!sites) + { + VectorSequenceContainer* sc = new VectorSequenceContainer(sequences->getAlphabet()); + for (unsigned int i = 0; i < sequences->getNumberOfSequences(); ++i) + { + auto_ptr seq(sequences->getSequence(i).clone()); + SequenceTools::removeStops(*seq); + sc->addSequence(*seq); + } + delete sequences; + sequences = sc; + } else { + VectorSiteContainer* sc = new VectorSiteContainer(sequences->getAlphabet()); + for (unsigned int i = 0; i < sequences->getNumberOfSequences(); ++i) + { + auto_ptr seq(sequences->getSequence(i).clone()); + SequenceTools::replaceStopsWithGaps(*seq); + sc->addSequence(*seq); + } + delete sequences; + sequences = sc; + } + } + + // +--------------+ + // | Remove stops | + // +--------------+ + else if (cmdName == "RemoveColumnsWithStop") + { + SiteContainer* sites = dynamic_cast(sequences); if (!sites) { - throw Exception("'RemoveStops' can only be used on alignment. You may consider using the 'CoerceToAlignment' command."); + throw Exception("'RemoveColumnsWithStop' can only be used on alignment. You may consider using the 'CoerceToAlignment' command."); } for (unsigned int i = sites->getNumberOfSites(); i > 0; i--) @@ -297,7 +331,12 @@ for (unsigned int i = 0; i < sequences->getNumberOfSequences(); i++) { BasicSequence seq = sequences->getSequence(i); + unsigned int len = seq.size(); SequenceTools::getCDS(seq, false, true, true, false); + if (aligned) { + for (unsigned int c = seq.size(); c < len; ++c) + seq.addElement(seq.getAlphabet()->getGapCharacterCode()); + } sc->addSequence(seq, false); } delete sequences; @@ -355,7 +394,7 @@ { map freqs; SiteTools::getFrequencies(sites->getSite(i - 1), freqs); - if (freqs[-1] >= gapFreq) sites->deleteSite(i - 1); + if (freqs[-1] > gapFreq) sites->deleteSite(i - 1); } } else @@ -388,6 +427,41 @@ delete sequences; sequences = sc; } + // +------------------+ + // | GetCodonPosition | + // +------------------+ + else if (cmdName == "GetCodonPosition") + { + unsigned int pos = ApplicationTools::getParameter("position", cmdArgs, 3); + OrderedSequenceContainer* sc = dynamic_cast(SequenceContainerTools::getCodonPosition(*sequences, pos - 1)); + delete sequences; + if (aligned) { + sequences = new VectorSiteContainer(*sc); + delete sc; + } else { + sequences = sc; + } + } + // +-----------------+ + // | FilterFromTree | + // +-----------------+ + else if (cmdName == "FilterFromTree") + { + auto_ptr tree(PhylogeneticsApplicationTools::getTree(cmdArgs, "")); + vector names = tree->getLeavesNames(); + OrderedSequenceContainer* reorderedSequences = 0; + if (aligned) { + reorderedSequences = new VectorSiteContainer(sequences->getAlphabet()); + } else { + reorderedSequences = new VectorSequenceContainer(sequences->getAlphabet()); + } + for (size_t i = 0; i < names.size(); ++i) { + reorderedSequences->addSequence(sequences->getSequence(names[i]), false); + } + delete sequences; + sequences = reorderedSequences; + } + else throw Exception("Unknown action: " + cmdName); } diff -Nru bppsuite-0.6.2/bppSuite/CMakeLists.txt bppsuite-0.7.0/bppSuite/CMakeLists.txt --- bppsuite-0.6.2/bppSuite/CMakeLists.txt 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/bppSuite/CMakeLists.txt 2012-02-15 22:04:28.000000000 +0000 @@ -42,6 +42,10 @@ TARGET_LINK_LIBRARIES(bpptreedraw ${LIBS}) SET_TARGET_PROPERTIES(bpptreedraw PROPERTIES LINK_SEARCH_END_STATIC ${BUILD_STATIC}) +ADD_EXECUTABLE(bppalnscore bppAlnScore.cpp) +TARGET_LINK_LIBRARIES(bppalnscore ${LIBS}) +SET_TARGET_PROPERTIES(bppalnscore PROPERTIES LINK_SEARCH_END_STATIC ${BUILD_STATIC}) + # Install progs INSTALL(TARGETS bppml @@ -54,4 +58,5 @@ bppreroot bppphysamp bpptreedraw + bppalnscore DESTINATION bin) diff -Nru bppsuite-0.6.2/bppSuite.spec bppsuite-0.7.0/bppSuite.spec --- bppsuite-0.6.2/bppSuite.spec 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/bppSuite.spec 2012-02-15 22:04:28.000000000 +0000 @@ -1,5 +1,5 @@ %define name bppsuite -%define version 0.6.1 +%define version 0.7.0 %define release 1 %define _prefix /usr @@ -29,6 +29,7 @@ - BppPhySamp for phylogenetic sampling, - BppReRoot for tree rerooting. - BppTreeDraw for tree drawing. + - BppAlnScore for comparing alignments and computing alignment scores. %prep %setup -q @@ -80,6 +81,10 @@ %{_prefix}/share/man/man1/bpptreedraw.1.gz %changelog +* Wed Feb 15 2012 Julien Dutheil +- BppSuite 0.7.0 release +* Thu Jun 09 2011 Julien Dutheil +- BppSuite 0.6.2 release * Mon Feb 28 2011 Julien Dutheil - BppSuite 0.6.1 release * Mon Feb 07 2011 Julien Dutheil diff -Nru bppsuite-0.6.2/ChangeLog bppsuite-0.7.0/ChangeLog --- bppsuite-0.6.2/ChangeLog 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/ChangeLog 2012-02-15 22:04:28.000000000 +0000 @@ -1,3 +1,12 @@ +08/02/12 -*- Version 0.7.0 -*- + +21/12/11 Julien Dutheil +* New bppAlnScore program +* Improved bppSeqMan: protein translation now works + more stop codons removal options. + +17/06/11 Julien Dutheil +* Improved bppancestor, also allows to compute frequencies for leaves. + 11/06/11 -*- Version 0.6.2 -*- * Small bug fixed + new packages. diff -Nru bppsuite-0.6.2/CMakeLists.txt bppsuite-0.7.0/CMakeLists.txt --- bppsuite-0.6.2/CMakeLists.txt 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/CMakeLists.txt 2012-02-15 22:04:28.000000000 +0000 @@ -164,9 +164,11 @@ COMMAND gzip -f bppphysamp.1 COMMAND cp bpptreedraw.1.txt bpptreedraw.1 COMMAND gzip -f bpptreedraw.1 + COMMAND cp bppalnscore.1.txt bppalnscore.1 + COMMAND gzip -f bppalnscore.1 WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man ) - SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "man/bppml.1.gz;man/bppseqgen.1.gz;man/bppdist.1.gz;man/bpppars.1.gz;man/bppseqman.1.gz;man/bppconsense.1.gz;man/bppancestor.1.gz;man/bppreroot.1.gz;man/bppphysamp.1.gz;man/bpptreedraw.1.gz") + SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "man/bppml.1.gz;man/bppseqgen.1.gz;man/bppdist.1.gz;man/bpppars.1.gz;man/bppseqman.1.gz;man/bppconsense.1.gz;man/bppancestor.1.gz;man/bppreroot.1.gz;man/bppphysamp.1.gz;man/bpptreedraw.1.gz;man/bppalnscore.1.gz") ENDIF(NROFF_EXE) # Subdirectories @@ -179,10 +181,10 @@ # Packager SET(CPACK_PACKAGE_NAME "bppsuite") SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team") -SET(CPACK_PACKAGE_VERSION "0.6.2") +SET(CPACK_PACKAGE_VERSION "0.7.0") SET(CPACK_PACKAGE_VERSION_MAJOR "0") -SET(CPACK_PACKAGE_VERSION_MINOR "6") -SET(CPACK_PACKAGE_VERSION_PATCH "2") +SET(CPACK_PACKAGE_VERSION_MINOR "7") +SET(CPACK_PACKAGE_VERSION_PATCH "0") SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt") SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt") @@ -215,6 +217,7 @@ "bppSuite/bpptreedraw" "bppSuite/bppdist" "bppSuite/bppseqgen" + "bppSuite/bppalnscore" "doc/bppsuite/" "doc/bppsuite\\\\.info" "doc/bppsuite\\\\.toc" diff -Nru bppsuite-0.6.2/debian/changelog bppsuite-0.7.0/debian/changelog --- bppsuite-0.6.2/debian/changelog 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/debian/changelog 2012-02-15 22:04:28.000000000 +0000 @@ -1,3 +1,10 @@ +bppsuite (0.7.0-1) unstable; urgency=low + + * Several program improvements (more models, options, etc.) + * New program bpp Alignment scores. + + -- Julien Dutheil Wed, 15 Feb 2012 09:17:00 +0100 + bppsuite (0.6.2-1) unstable; urgency=low * RFP: Bio++ -- The Bio++ bioinformatics libraries. (Closes: #616373). diff -Nru bppsuite-0.6.2/debian/control bppsuite-0.7.0/debian/control --- bppsuite-0.6.2/debian/control 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/debian/control 2012-02-15 22:04:28.000000000 +0000 @@ -4,12 +4,12 @@ Maintainer: Loic Dachary Uploaders: Julien Dutheil Build-Depends: debhelper (>= 5), cmake (>= 2.6), dpkg (>= 1.15.4) | install-info, texinfo, - libbpp-phyl-dev (>= 2.0.1) + libbpp-phyl-dev (>= 2.0.3) Standards-Version: 3.9.1 Package: bppsuite Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-phyl9 (>= 2.0.1) +Depends: ${shlibs:Depends}, ${misc:Depends}, libbpp-phyl9 (>= 2.0.3) Description: Bio++ program suite Includes programs: - BppML for maximum likelihood analysis, @@ -21,4 +21,6 @@ - BppConsense for building consensus tree and computing bootstrap values, - BppPhySamp for phylogenetic sampling, - BppReRoot for tree rerooting. + - BppTreeDraw for tree drawing. + - BppAlnScore for comparing alignments and computing alignment scores. diff -Nru bppsuite-0.6.2/doc/bppsuite.texi bppsuite-0.7.0/doc/bppsuite.texi --- bppsuite-0.6.2/doc/bppsuite.texi 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/doc/bppsuite.texi 2012-02-15 22:04:28.000000000 +0000 @@ -1,7 +1,7 @@ \input texinfo @c -*-texinfo-*- @c %**start of header @setfilename bppsuite.info -@settitle BppSuite Manual 0.6.0 +@settitle BppSuite Manual 0.7.0 @documentencoding UTF-8 @afourpaper @dircategory Science Biology Genetics @@ -15,16 +15,15 @@ * bppphysamp: (bppphysamp) Bio++ Phylogenetic Sampler. * bppreroot: (bppreroot) Bio++ Serial Tree Re-rooting. * bppseqman: (bppseqman) Bio++ Sequences Manipulation. +* bppalnscore: (bppalnscore) Bio++ Alignment Scoring * bpptreedraw: (bpptreedraw) Bio++ Tree Drawing. @end direntry @c %**end of header -@include version.texi - @copying -This is the manual of the Bio++ Program Suite, version @value{VERSION}, @value{UPDATED}. +This is the manual of the Bio++ Program Suite, version 0.6.0. -Copyright @copyright{} 2007, 2008, 2009, 2010, 2011 Bio++ development team +Copyright @copyright{} 2007, 2008, 2009, 2010, 2011, 2012 Bio++ development team @end copying @titlepage @@ -64,6 +63,7 @@ * Model:: Setting up a substitution model. * Estimation:: Estimating parameters by maximizing a likelihood function. * WritingSequences:: Writing sequences/alignments to files. +* WritingTrees:: Writing trees to files. Bio++ Program Suite Reference @@ -76,6 +76,7 @@ * bppphysamp:: Bio++ Phylogenetic Sampler. * bppreroot:: Bio++ Serial Tree Re-rooting. * bppseqman:: Bio++ Sequences Manipulation. +* bppalnscore:: Bio++ Alignment Scoring * bpptreedraw:: Bio++ Tree Drawing. @end detailmenu @@ -240,15 +241,15 @@ @example optimization.topology.algorithm = NNI optimization.topology.algorithm_nni.method = phyml -output.tree = MyData_$(optimization.topology.algorithm)_$(optimization.topology.algorithm_nni.method).dnd +output.tree.file = MyData_$(optimization.topology.algorithm)_$(optimization.topology.algorithm_nni.method).dnd @end example @end cartouche You can use this syntax to define global variables: @cartouche @example data=MyData -sequence.file=$(data).fasta -input.tree=$(data).dnd +input.sequence.file=$(data).fasta +input.tree.file=$(data).dnd output.infos=$(data).infos @end example @end cartouche @@ -261,8 +262,8 @@ @example #Option file 1: param=options2.bpp -sequence.file=$(data).fasta -sequence.format=Fasta +input.sequence.file=$(data).fasta +input.sequence.format=Fasta @end example @end cartouche @cartouche @@ -286,6 +287,7 @@ * Model:: Setting up a substitution model. * Estimation:: Estimating parameters by maximizing a likelihood function. * WritingSequences:: Writing sequences/alignments to files. +* WritingTrees:: Writing trees to files. @end menu @node Sequences, Tree, Common, Common @@ -293,10 +295,15 @@ @table @command @item alphabet = -@{DNA|RNA|Protein|Word(letter=@{DNA|RNA|Protein@},length=@{int@})| +@{DNA|RNA|Protein|Binary|Word(letter=@{DNA|RNA|Protein@},length=@{int@})| Codon(letter=@{DNA|RNA@}, type=@{Standard|EchinodermMitochondrial|InvertebrateMitochondrial|\ VertebrateMitochondrial@})@} -The alphabet to use when reading sequences. +The alphabet to use when reading sequences. DNA and RNA alphabet can in addition take an argument: + +@table @command +@item bangAsgap=@{bool@} +Tell is exclamation mark should be considered as a gap character. The default is to consider it as an unknown character such as 'N' or '?'. +@end table @item input.sequence.file=@{path@} The sequence file to use. Depending on the program, these sequences have or do not have to be aligned. @@ -310,8 +317,10 @@ @table @command -@item Fasta() +@item Fasta(extended=@{bool@}, strictNames=@{bool@}) The fasta format. +The argument @command{extended}, default to 'no', allows to enable the HUPO-PSI extension of the format. +The argument @command{strict_names}, default to 'no', specifies that only the first word in the fasta header is used as a sequence names, the rest of the header being considered as comments. @item Mase(siteSelection=@{chars@}) The Mase format (as read by Seaview and Phylo_win for instance), with an optional site selection name. @@ -379,7 +388,7 @@ @item input.tree.file = @{path@} The phylogenetic tree file to use. -@item input.tree.format = @{Newick|Nexus@} +@item input.tree.format = @{Newick|Nexus|NHX@} The format of the input tree file. @end table @@ -391,7 +400,7 @@ @item input.trees.file = @{path@} The file containing multiple trees. -@item input.trees.format = @{Newick|Nexus@} +@item input.trees.format = @{Newick|Nexus|NHX@} The format of the input tree file. @end table @@ -434,6 +443,28 @@ parameters. The following table lists the set of usable functions, and their parameters. +Many models have a set of optional parameters denoted here as +"equilibrium frequencies" that are used to initialize the parameters +of the model related with the equilibrium frequencies. These options +are: + +@table @command + +@item initFreqs=values(@{real]0,1[@},...,@{real]0,1[@}) +The equilibrium frequency is set equal (as much as possible) to the +given frequencies. Those frequencies are given in the same order as +the alphabet, and they must sum 1. + +@item initFreqs=observed +The equilibrium frequency is set equal (as much as possible) to the +observed frequencies. + +@item initFreqs.observedPseudoCount=@{integer@} +a peusocount integer added to all counts of letters (or words), when +the frequencies are computed from observed data. + +@end table + @subsubsection Nucleotide models @table @command @@ -441,39 +472,37 @@ @item JC69 The Jukes and Cantor model. This model has no additional parameter. -@item K80(kappa=@{real>0@}) -The Kimura 2 parameters model. @var{kappa} is the transition over transversion ratio. +@item K80([kappa=@{real>0@}]) +The Kimura 2 parameters model. @var{kappa} is the transition over +transversion ratio. Default: @var{kappa}=1 + +@item F84([kappa=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@},theta2=@{real]0,1[@} ,"equilibrium frequencies"] ) +Felsenstein's 1984 substitution model, with transition/transversion +ratio and 4 distinct equilibrium frequencies, set using three +independent parameters: @var{theta} is the GC content, @var{theta1} is +the proportion of G / (G + C) and @var{theta2} is the proportion of A +/ (A + T or U). + +@item HKY85([kappa=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@} ,"equilibrium frequencies"]) +Hasegawa, Kishino and Yano 1985's substitution model. The model is +similar to @command{F84}, but with a different implementation. The +@var{kappa} parameter used here is comparable to the one in +@command{K80}. + +@item T92([kappa=@{real>0@}, theta=@{real]0,1[@} ,"equilibrium frequencies"]) +Tamura 1992's model for nucleotides, similar to @command{HKY85}, yet +assuming that the frequencies of A = T/U and G = C. + +@item TN93([kappa1=@{real>0@}, kappa2=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@} ,"equilibrium frequencies"]) +Tamura and Nei 1993's model, similar to @command{HKY85}, but allowing +for two distinct transition/transversion ratios. + +@item GTR([a=@{real>0@}, b=@{real>0@}, c=@{real>0@}, d=@{real>0@}, e=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@} ,"equilibrium frequencies"]) +The General Time-Reversible substitution model. Parameters @var{a}, +@var{b}, @var{c}, @var{d}, @var{e} are the entries of the +exchangeability matrix. -@item F84(kappa=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) -Felsenstein's 1984 substitution model, with -transition/transversion ratio and 4 distinct equilibrium frequencies, -set using three independent parameters: @var{theta} is the GC content, -@var{theta1} is the proportion of G / (G + C) and @var{theta2} is the -proportion of A / (A + T or U). The @var{useObservedFreqs} option set -the @var{theta}s parameters according to the observed counts in the -data set, and @var{useObservedFreqs.pseudoCount} is a quantity, -defaulting to 0, that can be used in case some counts are zero, on -small data sets for instance. The corrected values are computed as: -@tex -$$\pi_i = {f_i + \psi \over 4\cdot\psi + \sum_j f_j}$$ -@end tex - -@item HKY85(kappa=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) -Hasegawa, Kishino and Yano 1985's substitution model. -The model is similar to @command{F84}, but with a different implementation. -The @var{kappa} parameter used here is comparable to the one in @command{K80}. - -@item T92(kappa=@{real>0@}, theta=@{real]0,1[@}, useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) -Tamura 1992's model for nucleotides, similar to @command{HKY85}, yet assuming that the frequencies of A = T/U and G = C. - -@item TN93(kappa1=@{real>0@}, kappa2=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) -Tamura and Nei 1993's model, similar to @command{HKY85}, but allowing for two distinct transition/transversion ratios. - -@item GTR(a=@{real>0@}, b=@{real>0@}, c=@{real>0@}, d=@{real>0@}, e=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) -The General Time-Reversible substitution model. -Parameters @var{a}, @var{b}, @var{c}, @var{d}, @var{e} are the entries of the exchangeability matrix. - -@item L95(beta=@{real>0@}, gamma=@{real>0@}, delta=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) +@item L95([beta=@{real>0@}, gamma=@{real>0@}, delta=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@} ,"equilibrium frequencies"]) The strand-symmetric model of Lobry 1995, for nucleotides. @end table @@ -497,57 +526,72 @@ @item LG08 Protein substitution model, from Le & Gascuel 2008. -@item LLG08_EX2(relrate1=@{real]0,1[@}, relproba1=@{real]0,1[@}) +@item LLG08_EX2([relrate1=@{real]0,1[@}, relproba1=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. -@item LLG08_EX3(relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}) +@item LLG08_EX3([relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. -@item LLG08_EHO(relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}) +@item LLG08_EHO([relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. -@item LLG08_UL2(relrate1=@{real]0,1[@}, relproba1=@{real]0,1[@}) +@item LLG08_UL2([relrate1=@{real]0,1[@}, relproba1=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. -@item LLG08_UL3(relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}) +@item LLG08_UL3([relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. -@item DSO78+F(theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) +@item DSO78+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ... ,"equilibrium frequencies"]) Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005 and free equilibrium frequencies. The @var{thetaX} are frequencies parameters, where X is 1 to 19. Parameter @var{theta1} is the proportion of A, @var{theta2} is the proportion of R over (1-A), @var{theta3} the proportion of N over (1-A-R), etc. -@item JTT92+F(theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) +@item JTT92+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005 and free equilibrium frequencies. -@item WAG01+F(theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) +@item WAG01+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Protein substitution model, from Whelan & Goldman 2001, and free equilibrium frequencies. -@item LG08+F(theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) +@item LG08+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Protein substitution model, from Le & Gascuel 2008, and free equilibrium frequencies. @item Empirical(name=@{chars@}, file=@{path@}) -Build a protein substitution model from a file in PAML format, and use 'name' as a namespace for parameters. +Build a protein substitution model from a file in PAML format, and use +'name' as a namespace for parameters. + +@item Empirical+F(name=@{chars@}, file=@{path@}, [theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) +Build a protein substitution model from a file in PAML format, and use +free equilibrium frequencies. 'name' will be used as a parameter +namespace, including for frequencies. + +@end table + +@subsubsection Miscellaneous models -@item Empirical+F(name=@{chars@}, file=@{path@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., useObservedFreqs=@{boolean@}, useObservedFreqs.pseudoCount=@{int>0@}) -Build a protein substitution model from a file in PAML format, and use free equilibrium frequencies. 'name' will be used as a parameter namespace, including for frequencies. +@table @command +@item Binary([kappa=@{real>0@} ,"equilibrium frequencies"]) +Build the model on binary alphabet, where @var{kappa} is the relative +proportion of 1 over 0 in the equilibrium distribution. Default: +@var{kappa}=1. @end table @subsubsection Codon models -Standard codon models: the optional @var{genetic_code} argument describes the genetic code. If -it is not given, the one related with the alphabet is used. The several values available are described below. +Standard codon models: the optional @var{genetic_code} argument +describes the genetic code. If it is not given, the one related with +the alphabet is used. The several values available are described +below. @itemize @item EchinodermMitochondrialGeneticCode @@ -557,9 +601,11 @@ @item YeastMitochondrialGeneticCode @end itemize -The next codon models also take as argument a @var{frequencies} option -specifying the equilirium frequencies of the model. Any frequencies description can be used here, but the syntax also supports -options similar to the ones used in the PAML software: +The next codon models also take as argument a @var{frequencies} option +specifying the equilibrium frequencies of the model. Any frequencies +description can be used here, but the syntax also supports options +similar to the ones used in the PAML software: + @itemize @item F0: all frequencies are assumed to be fixed and equal to 1/61, 0 for stop codons. @item F1X4: 4 distinct frequencies are used, with parameters theta, theta1, theta2 (@xref{Frequencies sets}, ``Full'' method). @@ -568,38 +614,38 @@ @end itemize The same words can be used to specify root frequencies for codon -models, in the case of non reversibility. +models, in the case of non stationarity. @table @command -@item GY94([genetic_code=@{genetic code description@} , kappa=@{real>0@}, V=@{real>0@}]) +@item GY94([genetic_code=@{genetic code description@}, kappa=@{real>0@}, V=@{real>0@}, "equilibrium frequencies"]) Goldman and Yang (1994) substitution model for codons (default values: @var{kappa}=1 and @var{V}=10000). -@item MG94([genetic_code=@{genetic code description@}, rho=@{real>0@}]) +@item MG94([genetic_code=@{genetic code descrition@}, rho=@{real>0@}, "equilibrium frequencies"]) Muse and Gaut (1994) substitution model for codons (default values: @var{rho}=1). -@item YN98([genetic_code=@{genetic code description@}, kappa=@{real>0@}, omega=@{real>0@}]) +@item YN98([genetic_code=@{genetic code description@}, kappa=@{real>0@}, omega=@{real>0@}, "equilibrium frequencies"]) Yang and Nielsen (1998) substitution model for codons (default values: @var{kappa}=1 and @var{omega}=1). -@item YNGKP_M0([genetic_code=@{genetic code description@}, kappa=@{real>0@}, omega=@{real>0@}]) +@item YNGKP_M0([genetic_code=@{genetic code description@}, kappa=@{real>0@}, omega=@{real>0@}, "equilibrium frequencies"]) The M0 model of PAML, ie the same as YN98. -@item YNGKP_M1([genetic_code=@{genetic code description@},kappa=@{real>0@}, omega=@{real>0@}, p0=@{real>0 and <1 @}]) +@item YNGKP_M1([genetic_code=@{genetic code description@},kappa=@{real>0@}, omega=@{real>0@}, p0=@{real>0 and <1 @}, "equilibrium frequencies"]) The M1a model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000) (default values: @var{kappa}=1, @var{p0}=0.5, @var{omega}=0.5). -@item YNGKP_M2([genetic_code=@{genetic code description@},kappa=@{real>0@}, omega0=@{real>0 and <1@}, theta1=@{real>0 and <1 @}], omega1=@{real>1@}, theta2=@{real>0 and <1 @}]) +@item YNGKP_M2([genetic_code=@{genetic code description@},kappa=@{real>0@}, omega0=@{real>0 and <1@}, theta1=@{real>0 and <1 @}], omega1=@{real>1@}, theta2=@{real>0 and <1 @}, "equilibrium frequencies"]) The M2a model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with p0=theta1 and p1=(1-theta1)*theta2 (default values: @var{kappa}=1, @var{theta1}=0.33333, @var{theta2}=0.5, @var{omega0}=0.5, @var{omega2}=0.5). -@item YNGKP_M3(genetic_code=@{genetic code description@}, n=@{integer>0@}, kappa=@{real>0@}, omega0=@{real>0 and <1@}, delta1=@{real>0@}, ..., delta@var{n-1}=@{real>0@}, theta1=@{real>0 and <1 @}, ..., theta@var{n-1}1=@{real>0 and <1 @}]) +@item YNGKP_M3([genetic_code=@{genetic code description@}, n=@{integer>0@}, kappa=@{real>0@}, omega0=@{real>0 and <1@}, delta1=@{real>0@}, ..., delta@var{n-1}=@{real>0@}, theta1=@{real>0 and <1 @}, ..., theta@var{n-1}1=@{real>0 and <1 @}, "equilibrium frequencies"]) The M3 model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with @var{n} discrete values, with p0=theta1 @@ -607,13 +653,13 @@ omegak=omega0+delta1+....+deltak (default values: @var{n}=3, @var{kappa}=1, @var{thetak}=1/(n-k+1), @var{omega0}=0.5, @var{deltak}=0.5). -@item YNGKP_M7(n=@{integer>0@}, [genetic_code=@{genetic code description@},kappa=@{real>0@}, p=@{real>1@}, q=@{real>1 @}]) +@item YNGKP_M7(n=@{integer>0@}, genetic_code=@{genetic code description@},kappa=@{real>0@}, p=@{real>1@}, q=@{real>1 @}, "equilibrium frequencies"]) The M7 model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with the Beta distribution discretized in @var{n} classes (default values: @var{kappa}=1, @var{p}=2, @var{q}=2). -@item YNGKP_M7(n=@{integer>0@}, [genetic_code=@{genetic code description@},kappa=@{real>0@}, omegas=@{real>1@}, p0=@{real>0@},p=@{real>1@}, q=@{real>1 @}]) +@item YNGKP_M8(n=@{integer>0@}, [genetic_code=@{genetic code description@},kappa=@{real>0@}, omegas=@{real>1@}, p0=@{real>0@},p=@{real>1@}, q=@{real>1 @}, "equilibrium frequencies"]) The M8 model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with the Beta distribution discretized in @var{n} @@ -622,115 +668,112 @@ @end table -It is also possible to setup more specific models, by specifying a nucleotide model for each position. -Model parameters names then take the form of CodonModel._.. - -@table @command - -@item CodonNeutral(model=@{model name@} [, relrate1=@{real>0@}, relrate2=@{real>0@}]) -or -@item CodonNeutral(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}[, relrate1=@{real>0@}, relrate2=@{real>0@}]) +It is also possible to setup more specific models, by specifying a +nucleotide model for each position. Model parameters names then take +the form of ._.. -Substitution model on codons. The arguments @var{model} and -@var{model@{i@}} are for descriptions of models on bases. The alphabet -must be a codon alphabet. +In the following models, the arguments @var{model} and +@var{model@{i@}} are for descriptions of models on bases. -If the argument is @var{model}, the @emph{same} single site model is +@itemize +@item If the argument is @var{model}, the @emph{same} single site model is used on all positions (ie the parameters are shared between all positions). - -If the arguments are @var{model1}, @var{model2}, @var{model3}, each +@item If the arguments are @var{model1}, @var{model2}, @var{model3}, each single site model stands for a single-site substitution model. In that case, all single site models parameters are position dependent. +@end itemize Each single site model is normalized and the substitution rates between codons that differ on more than one letter are null. -Arguments @var{relrate@{i@}} stands for the relative substitution rates -of the sites. Default: @var{relrate@{i@}=1/@{4-i@}}, such that the rate -of each site is 1/3. - The generator is first computed with these models and parameters on the whole triplet alphabet, and then the substitution rates to and from stop codons are set to zero and the generator is normalized with this modification. +@table @command + +@item CodonRate(model=@{model name@} [, relrate1=@{real>0@}, relrate2=@{real>0@}, "equilibrium frequencies"]) + +or + +@item CodonRate(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}[, relrate1=@{real>0@}, relrate2=@{real>0@}, "equilibrium frequencies"]) + +Substitution model on codons with position specific evolution rates. + +Arguments @var{relrate@{i@}} stands for the relative substitution rates +of the sites. Default: @var{relrate@{i@}=1/@{4-i@}}, such that the rate +of each site is 1/3. + @example alphabet=Codon(letter=DNA, type=Standard) -model=CodonNeutral(model=T92) +model=CodonRate(model=T92) @end example builds a model on codons, such all sites follow the same T92 model. -The parameters names are @var{CodonNeutral.123_T92.kappa}, -@var{CodonNeutral.relrate1}, @var{CodonNeutral.relrate2}. +The parameters names are @var{CodonRate.123_T92.kappa}, +@var{CodonRate.relrate1}, @var{CodonRate.relrate2}. @example alphabet=Codon(letter=DNA, type=Standard) -model=CodonNeutral(model1=T92, model2=T92, model3=JC69) +model=CodonRate(model1=T92, model2=T92, model3=JC69) @end example builds a model on codons, such that first and second sites follow independent T92 models, and third site follows a JC69 model. Then the -parameters names are @var{CodonNeutral.1_T92.kappa}, -@var{CodonNeutral.2_T92.kappa}, @var{CodonNeutral.relrate1}, -@var{CodonNeutral.relrate2}, and can be initialized as is: +parameters names are @var{CodonRate.1_T92.kappa}, +@var{CodonRate.2_T92.kappa}, @var{CodonRate.relrate1}, +@var{CodonRate.relrate2}, and can be initialized as is: @example -model=CodonNeutral(model1=T92, model2=T92, model3=JC69,\ - 1_T92.theta=0.5, 1_T92.kappa=2.0, 2_T92.theta=0.4, 2_T92.kappa=2.0) +model=CodonRate(model1=T92(theta=0.5, kappa=2), \ + model2=T92(theta=0.4, kappa=2), model3=JC69) @end example -@item CodonAsynonymous(model=@{model name@}[, genetic_code=@{genetic code description@}, beta=@{real>0@}]) +@item CodonDistance(model=@{model name@}[, genetic_code=@{genetic code description@}, beta=@{real>0@}, "equilibrium frequencies"]) or -@item CodonAsynonymous(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}[, geneticcode=@{genetic code description@}, beta=@{real>0@}]) +@item CodonDistance(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}[, geneticcode=@{genetic code description@}, beta=@{real>0@}, "equilibrium frequencies"]) -substitution model on codons. - -The arguments @var{model} and @var{model@{i@}} are for descriptions of -models on bases. The alphabet must be a codon alphabet. - -If the argument is @var{model}, the @emph{same} single site model is -used on all positions (ie the parameters are shared between all -positions). - -If the arguments are @var{model1}, @var{model2}, @var{model3}, each -single site model stands for a single-site substitution model. In that -case, all single site models parameters are position dependent. - -Each single site model is normalized and the substitution rates -between codons that differ on more than one letter are null. - -In addition to these models, the optional @var{geneticcode} argument -describes the genetic code. If it is not given, the one related with -the alphabet is used. The several values available are described -below. +Substitution model on codons that takes into account the difference +between synonymous and non-synonymous substitutions. Optional argument @var{beta} is the ratio between non-synonymous substitution rate and synonymous substitution rate. Default value: 1. @example alphabet=Codon(letter=DNA, type=Standard) -model=CodonAsynonymous(model=T92) +model=CodonDistance(model=T92) @end example builds a model on codons, such all sites follow the same T92 model. -The parameters names are @var{CodonAsynonymous.123_T92.kappa} and -@var{CodonAsynonymous.beta}. +The parameters names are @var{CodonDistance.123_T92.kappa} and +@var{CodonDistance.beta}. @example alphabet=Codon(letter=DNA, type=Standard) -model=CodonNeutral(model1=T92, model2=T92, model3=JC69) +model=CodonDistance(model1=T92, model2=T92, model3=JC69) @end example builds a model on codons, such that first and second sites follow independent T92 models, and third site follows a JC69 model. Then the -parameters names are @var{CodonAsynonymous.1_T92.kappa}, -@var{CodonAsynonymous.2_T92.kappa}, @var{CodonAsynonymous.beta}. +parameters names are @var{CodonDistance.1_T92.kappa}, +@var{CodonDistance.2_T92.kappa}, @var{CodonDistance.beta}. + +@item CodonRateFrequencies(model=@{model name@}, frequencies=@{frequencies set description@}[, relrate1=@{real>0@}, relrate2=@{real>0@}, "equilibrium frequencies"]) +or +@item CodonRateFrequencies(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}, frequencies=@{frequencies set description@} [, relrate1=@{real>0@}, relrate2=@{real>0@}, "equilibrium frequencies"]) -@item CodonNeutralFrequencies(frequencies=@{frequencies set description@} [, relrate1=@{real>0@}, relrate2=@{real>0@}]) -substitution model on codons. The exchangeability model on each site -is the same K80 model, and the equilibrium distribution of the model -is description by the @var{frequencies} argument. See the description -of the Frequencies Set below. +Substitution model on codons with position specific evolution rates, +where the sustitution rates are multiplied by the frequency of the +target codon in the given frequencies set. + +This model should be used with nucleotidic models which equilibrium +distribution is fixed, ans does not depend on the parameters. +Otherwise there may be problems of identifiability of the parameters. + +The multiplicative distribution of the model is described by the +@var{frequencies} argument. See the description of the Frequencies Set +below. Each single site model is normalized and the substitution rates between codons that differ on more than one letter are null. @@ -739,53 +782,69 @@ of the sites. Default: @var{relrate@{i@}=1/@{4-i@}}, such that the rate of each site is 1/3. -The generator is first computed with these model and distribution on -the whole triplet alphabet, and then the substitution rates to and -from stop codons are set to zero and the generator is normalized with -this modification. - @example alphabet=Codon(letter=DNA, type=Standard) -model=CodonNeutralFrequencies(frequencies=Full()) +model=CodonRateFrequencies(frequencies=Full()) @end example -has parameters @var{CodonNeutralFrequencies.123_K80.kappa}, -@var{CodonNeutralFrequencies.Full.theta_1}, ..., -@var{CodonNeutralFrequencies.Full.theta_60}, -@var{CodonNeutralFrequencies.relrate1}, -@var{CodonNeutralFrequencies.relrate2}. - -@item CodonAsynonymousFrequencies(frequencies=@{frequencies set description@} [geneticcode=@{genetic code description@}, beta=@{real>0@}]) - -substitution model on codons. The exchangeability model on each site -is the same K80 model, and the equilibrium distribution of the model -is description by the @var{frequencies} argument. See the description -of the Frequencies Set below. +has parameters @var{CodonRateFrequencies.123_K80.kappa}, +@var{CodonRateFrequencies.Full.theta_1}, ..., +@var{CodonRateFrequencies.Full.theta_60}, +@var{CodonRateFrequencies.relrate1}, +@var{CodonRateFrequencies.relrate2}. -Each single site model is normalized and the substitution rates -between codons that differ on more than one letter are null. +@item CodonDistanceFrequencies(model=@{model name@}, frequencies=@{frequencies set description@} [geneticcode=@{genetic code description@}, beta=@{real>0@}, "equilibrium frequencies"]) -In addition to these models, the optional @var{geneticcode} argument -describes the genetic code. If it is not given, the one related with -the alphabet is used. The several values available are described +or + +@item CodonDistanceFrequencies(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}, frequencies=@{frequencies set description@} [geneticcode=@{genetic code description@}, beta=@{real>0@}, "equilibrium frequencies"]) + +Substitution model on codons that takes into account the difference +between synonymous and non-synonymous substitutions. Moreover, the +sustitution rates are multiplied by the frequency of the target codon +in the given frequencies set. + +This model should be used with nucleotidic models which equilibrium +distribution is fixed, ans does not depend on the parameters. +Otherwise there may be problems of identifiability of the parameters. + +The multiplicative distribution of the model is described by the +@var{frequencies} argument. See the description of the Frequencies Set below. Optional argument @var{beta} is the ratio between non-synonymous substitution rate and synonymous substitution rate. Default value: 1. -The generator is first computed with these model and distribution on -the whole triplet alphabet, and then the substitution rates to and -from stop codons are set to zero and the generator is normalized with -this modification. - @example alphabet=Codon(letter=DNA, type=Standard) -model=CodonAsynonymousFrequencies(frequencies=Full()) +model=CodonDistanceFrequencies(frequencies=Full()) @end example -has parameters @var{CodonAsynonymousFrequencies.012_T92.kappa}, -@var{CodonAsynonymousFrequencies.Full.theta_1}, ..., -@var{CodonAsynonymousFrequencies.Full.theta_60}, -@var{CodonAsynonymousFrequencies.beta}. +has parameters @var{CodonDistanceFrequencies.012_T92.kappa}, +@var{CodonDistanceFrequencies.Full.theta_1}, ..., +@var{CodonDistanceFrequencies.Full.theta_60}, +@var{CodonDistanceFrequencies.beta}. + +@item CodonDistancePhaseFrequencies(model=@{model name@}, frequencies=@{frequencies set description@} [geneticcode=@{genetic code description@}, beta=@{real>0@}, "equilibrium frequencies"]) + +or + +@item CodonDistancePhaseFrequencies(model1=@{model name@}, model2=@{model name@}, model3=@{model name@}, frequencies=@{frequencies set description@} [geneticcode=@{genetic code description@}, beta=@{real>0@}, "equilibrium frequencies"]) +Substitution model on codons that takes into account the difference +between synonymous and non-synonymous substitutions. Moreover, the +sustitution rates are multiplied by the product of the frequencies of +the changed nucleotides -- conditioned on the phase -- in the given +frequencies set. + +This model should be used with nucleotidic models which equilibrium +distribution is fixed, ans does not depend on the parameters. +Otherwise there may be problems of identifiability of the parameters. + +The multiplicative distribution of the model is described by the +@var{frequencies} argument. See the description of the Frequencies Set +below. + +Optional argument @var{beta} is the ratio between non-synonymous +substitution rate and synonymous substitution rate. Default value: 1. @end table @@ -795,9 +854,9 @@ @table @command -@item Word(model=@{model name@} [,relrate1=@{1>real>0@}, ..., relrate@{n-1@}=@{1>real>0@}]) +@item Word(model=@{model name@} [,relrate1=@{1>real>0@}, ..., relrate@{n-1@}=@{1>real>0@}, "equilibrium frequencies"]) or -@item Word(model1=@{model name@}, model1=@{model name@}, ..., modeln=@{model name@}[, relrate1=@{1> real>0@}, ..., relrate@{n-1@}=@{1> real>0@}]) +@item Word(model1=@{model name@}, model1=@{model name@}, ..., modeln=@{model name@}[, relrate1=@{1> real>0@}, ..., relrate@{n-1@}=@{1> real>0@}, "equilibrium frequencies"]) substitution model on words. The arguments @var{model} and @var{model@{i@}} are for descriptions of models on single sites such @@ -830,7 +889,8 @@ @example alphabet=Word(letter=DNA,length=4) -model=Word(model1=T92(), model2=T92(), model3=JC69(), model4=HKY85()) +model=Word(model1=T92(), model2=T92(), model3=JC69(), \ + model4=HKY85()) @end example builds a model on 4 bases words, such first and second sites follow independent T92 models, third site follows a JC69 model, and fourth @@ -892,35 +952,37 @@ @table @command -@item TS98(model=@{model description@}, s1=@{real>0@}, s2=@{real>0@}) +@item TS98(model=@{model description@}, s1=@{real>0@}, s2=@{real>0@} [, "equilibrium frequencies"]) Tuffley and Steel 1998's 'covarion' model, taking a nested substitution model as argument for @var{model}. The nested model can be any substitution model for any alphabet. -@item G01(model=@{model description@}, rdist=@{rate distribution description@}, mu=@{real>0@}) +@item G01(model=@{model description@}, rdist=@{rate distribution description@}, mu=@{real>0@} [, "equilibrium frequencies"]) Galtier 2001's 'covarion' model, taking a nested substitution model as argument for @var{model} and a rate distribution for parameter @var{rdist} (see below). The nested model can be any substitution model for any alphabet. -@item RE08(model=@{model description@}, lambda=@{real>0@}, mu=@{real>0@}) +@item RE08(model=@{model description@}, lambda=@{real>0@}, mu=@{real>0@} [, "equilibrium frequencies"]) Rivas and Eddy 2008's substitution model with gaps, taking a nested substitution model as argument for @var{model}. Parameter @var{lambda} is the insertion rate, while @var{mu} is the deletion rate. @end table -@subsubsection Mixture of models (beta feature) +@subsubsection Mixture of models @table @command -Mixed models combine any sustitution models with a priori distribution -of parameters. Such models are still experimental and have not been -yet fully tested. They should hence be used wih extra care! +Mixed models combine any substitution models with a priori +distribution of parameters. We call submodels all the models that are +mixed in the mixture. During the likelihood computation process, all the submodels of the mixture are successively applied on the branches, and the mean of all the likelihoods is computed. With nonhomogeneous reconstruction, since a mixed model is a random variable, affecting a mixed model to a set of branches means that all these branches are dependent, and in this -case all the branches of the set have the same submodel at the same -time. +case a site follows the same submodels in all the branches of the set +that support this mixed model. Moreover, it is possible to define +paths that define dependencies between submodels of different +mixtures (see below). @item MixedModel(model=@{model description@}) Mixture model from a given @var{model} in which some parameters follow @@ -939,7 +1001,7 @@ @var{TN93.theta}, @var{MixedModel.TN93.theta1}, @var{TN93.theta2}. -@item Mixture(model1=@{model description@},..., modeln=@{model description@} [, relrate1=@{1>real>0@},..., relrate@{n-1@}=@{1>real>0@}, relproba1=@{1>real>0@}, ..., relproba@{n-1@}=@{1>real>0@}]) +@item Mixture(model1=@{model description@},..., modeln=@{model description@} [, relrate1=@{1>real>0@},..., relrate@{n-1@}=@{1>real>0@}, relproba1=@{1>real>0@}, ..., relproba@{n-1@}=@{1>real>0@}, "equilibrium frequencies"]) Mixture model built from several @var{models}: each model has its own probability and rate. @@ -957,6 +1019,7 @@ @var{Mixture.2_YN98.kappa}, @var{Mixture.2_YN98.omega}. @end table + @subsubsection Linking parameters It is possible to reduce the parameter space by putting extra constraints on parameters, using for instance @@ -1034,15 +1097,17 @@ @example model1 = T92(theta=0.4, kappa=4) model2 = GTR(theta=0.4, a = 1.1, b=0.4, c=0.4, d=0.25, e=0.1) -nonhomogeneous.alias=GTR.theta_1->T92.theta_1 +nonhomogeneous.alias=GTR.theta1->T92.theta1 @end example This option can be used to link parameters of the root frequencies if the model is non-stationary: @example nonhomogeneous.root_freq=Full(init=balanced) -nonhomogeneous.alias=Full.theta->GTR.theta_1 +nonhomogeneous.alias=Full.theta1->GTR.theta1_1 @end example +Note that this option is only available with the 'general' nonhomogeneous substitution models and will be ignored if used with "one_per_branch". + @end table Finally, you may find useful the following options: @@ -1055,23 +1120,121 @@ The use of that option will cause the program to exit just after producing the tagged tree. @item output.parameter_names.file = @{@{path@}|none@} -A text file listing all parameter names. This might come handy in order to specify the parameter that should not be optimized (see optimization.ignore_parameter) or aliased (see above). -The use of that option will cause the program to exit just after producing the list file. +A text file listing all parameter names. This might come handy in +order to specify the parameter that should not be optimized (see +optimization.ignore_parameter) or aliased (see above). The use of that +option will cause the program to exit just after producing the list +file. @end table +@subsubsection Paths among non-homogeneous mixture models + +To define constraints for sites between submodels, we can set "paths" +that any site must follow. For example, in the following description: + +@example +nonhomogeneous = general +nonhomogeneous.number_of_models = 3 + +model1=T92() +model2=MixedModel(model=T92(kappa=Simple(values=(4,10,20),probas=(0.1,0.5,0.4)))) +model3=MixedModel(model=TN93(theta1=Simple(values=(0.1,0.5,0.9),probas=(0.3,0.2,0.5)))) + +model1.nodes_id=0:1 +model2.nodes_id=2:3 +model3.nodes_id=4:5 +@end example + +In this case, on branches 2 & 3 a site follows any submodel of model 2 +(but the same submodel on both branches), and on branches 4 & 5, a +site follows any submodel of model 3 (the same on both branches as +well). But there is no constraint between models 2 & 3, which means +that a site can follow any submodel of model 2 and any submodel of +model 3. + +If the user wants that a site with @var{T92.kappa=4} in model 2 has +@var{TN93.theta1=0.1} in model 3, that a site with @var{T92.kappa=10} +in model 2 has @var{TN93.theta1=0.9} in model 3, and that other cases +are free (in this case it means that @var{T92.kappa=20} in model 2 is +linked with @var{TN93.theta1=0.5} in model 3), then we can use the +declarations: + +@example +site.number_of_paths=2 +site.path1=model2[T92.kappa_1] & model3[TN93.theta1_2] +site.path2=model2[T92.kappa_2] & model3[TN93.theta1_3] +@end example + +The third path (for the remaining submodels) is automatically +computed. + +It is possible to link mixtures of submodels. For example, + +@example +site.path1=model2[T92.kappa_1] & model3[TN93.theta1_2] & model3[TN93.theta1_3] +@end example + +means that a site that has @var{T92.kappa=4} in model2 has either +@var{TN93.theta1=0.5} or @var{TN93.theta1=0.9} in model3. + + +Because of these constraints, the probabilities of the submodels are +linked. In the first example, probability of @var{T92.kappa=4} in +model 2 equals the probability of @var{TN93.theta1=0.5} in model 3. +Since it is contradictory with the probabilities defined in models 2 +or 3, the reference probabilities are the ones of the first numbered +mixed model, here model 2. In this case, the probabilities in model 3 +may have no use, but with the second example the probability of +submodel T92.kappa=4 equals the sum of the probabilities of submodels +TN93.theta1=0.5 or TN93.theta1=0.9. The relative proportion of those +models used in the declaration of model 3 is then used. Here their +respective probabilities are then: 0.1*0.2/ (0.2+0.5)=0.0286 and +0.1*0.5/(0.2+0.5)=0.0714. + +Concerning the optimization procedure, this choice may entail the non- +identifiability of several parameters (here the probabilities in model +3), so the user should be careful about this. + +Another example in the case of mixtures of mixed models, where the +submodels are defined by their names; + +@example +nonhomogeneous = general +nonhomogeneous.number_of_models = 2 + +model1=LLG08_UL2() +model2=LLG08_UL3() + +site.number_of_paths=2 +site.path1=model1[LLG08_UL2.M2] & model2[LLG08_UL3.Q1] +site.path2=model1[LLG08_UL2.M1] & model2[LLG08_UL3.Q2] & model2[LLG08_UL3.Q3] +@end example + +When nonhomogeneity option is @option{one_per_branch}, each site is +constrained to follow the same submodel from leaves to root. + @subsubsection Root frequencies -In case of nonstationary models, the ancestral frequencies are distinct parameters. If a model is assumed to be stationary, -the ``None'' parameter value can be used, which is strictly equivalent to setting +In case of nonstationary models, the ancestral frequencies are +distinct parameters. If a model is assumed to be stationary, the +``None'' parameter value can be used, which is strictly equivalent to +setting @command{nonhomogeneous.stationary=yes}. -As since version 0.4.0, BppSuite uses the keyval syntax to set up root frequencies, +When the model is a mixture model, since there is not a set of +equilibrium frequencies, with this option the root frequencies are set +to be the average (with the respective probabilities of the submodels) +of the equilibrium frequencies of the submodels. + +As since version 0.4.0, BppSuite uses the keyval syntax to set up root +frequencies, @table @command @item nonhomogeneous.root_freq=@{frequency set description@} @end table -The Frequencies set used can be any of the ones described below @xref{Frequencies sets}, depending on the alphabet used. +The Frequencies set used can be any of the ones described below +@xref{Frequencies sets}, depending on the alphabet used. @subsection Frequencies sets @@ -1132,9 +1295,53 @@ @var{Word.2_GC.theta}, @var{Word.4_Full.theta_1}, @var{Word.4_Full.theta_2}, @var{Word.4_Full.theta_3}. +@item Codon(frequency=@{frequency set description@}) + +or + +@item Codon(frequency1=@{frequency set description@}, frequency2=@{frequency set description@}, frequency3=@{frequency set description@}) + +frequencies on codons computed as the product of frequencies on the +letters, with stop codon frequencies set to zero. The arguments +@var{frequency} and @var{frequency@{i@}} are for descriptions of +frequency sets on nucleotides. The alphabet must be a Codon alphabet. + +If the argument is @var{frequency}, the @emph{same} single site +frequency set is used (ie the parameters are shared between all +positions). + +If the arguments are @var{frequency1}, @var{frequency2}, +@var{frequency3}, all single site frequency sets are independent. In +that case, all single site frequency set parameters are position +dependent. + +@example +alphabet=Codon(letter=DNA, type=Standard) +Codon(frequency=GC()) +@end example +builds a frequency set on codons, such that all sites frequencies +follow the same GC frequency set model. The parameter name is +@var{Codon.123_GC.theta}. + +@example +alphabet=Codon(letter=DNA, type=Standard) +Codon(frequency1=GC(),frequency2=GC(),frequency3=Fixed()) +@end example + +builds a frequency set on codons, such that first and second sites +follow independent GC frequency sets, third site follows a Fixed +frequency set. Then the parameters names are @var{Codon.1_GC.theta}, +@var{Codon.2_GC.theta}. + + +Predefined codon frequencies are available, with a syntax similar to +the one used in the PAML software. See above Codon Models section. + @end table -All functions accept the following arguments, that take priority over the parameter specification: +All functions accept the following arguments, that take priority over +the parameter specification: + @table @command @item init=@{balanced,observed@} @@ -1145,7 +1352,9 @@ added to all the counts. @item values=(@{vector@}) -Explicitly set all frequencies manually. The size of the input vector should equal the number of resolved states in the alphabet, be in alphabetical order of states, and sum to one. +Explicitly set all frequencies manually. The size of the input vector +should equal the number of resolved states in the alphabet, be in +alphabetical order of states, and sum to one. @end table @@ -1282,7 +1491,7 @@ @table @command @item None - (no optimization is performed, initial values are kept ``as is''. +No optimization is performed, initial values are kept ``as is''. @item FullD(derivatives=@{Newton|Gradient@}) Full-derivatives method. Branch length derivatives are computed @@ -1352,9 +1561,6 @@ @item optimization.tolerance = @{float>0@} The precision on the log-likelihood to reach. -@item output.tree.file = @{@{path@}|none@} -File path where to write the optimized tree. - @item output.infos = @{@{path@}|none@} A text file containing several statistics for each site in the alignment. @@ -1362,9 +1568,11 @@ @end table +The resulting tree will be written to a file specified by the general tree writing options (@ref{WritingTrees}). + @c ------------------------------------------------------------------------------------------------------------------ -@node WritingSequences, , Estimation, Common +@node WritingSequences, WritingTrees, Estimation, Common @section Writing sequences/alignments to files @table @command @@ -1381,6 +1589,32 @@ @c ------------------------------------------------------------------------------------------------------------------ +@node WritingTrees, , WritingSequences, Common +@section Writing trees to files + +@table @command +@item output.tree.file = @{path@} +The phylogenetic tree file to write to. + +@item output.tree.format = @{Newick|Nexus|NHX@} +The format of the output tree file. + +@end table + +Some programs may require that you write multiple trees to a file. +The corresponding options are then: + +@table @command +@item output.trees.file = @{path@} +The file that will contain multiple trees. + +@item output.trees.format = @{Newick|Nexus|NHX@} +The format of the output tree file. + +@end table + +@c ------------------------------------------------------------------------------------------------------------------ + @node Reference, , Common, Top @chapter Bio++ Program Suite Reference @@ -1400,6 +1634,7 @@ * bppphysamp:: Bio++ Phylogenetic Sampler. * bppreroot:: Bio++ Serial Tree Re-rooting. * bppseqman:: Bio++ Sequences Manipulation. +* bppalnscore:: Bio++ Alignment Scoring * bpptreedraw:: Bio++ Tree Drawing. @end menu @@ -1495,7 +1730,7 @@ @table @command -@item optimize.clock=@{no|global@} +@item optimization.clock=@{no|global@} Tell if a molecular clock should be assumed. Topology estimation is not possible with a clock constraint. @@ -1583,8 +1818,8 @@ Specific options are: @table @command -@item asr.method = @{marginal@} -That's the only option for now! +@item asr.method = @{none|marginal@} +Marginal is the only option for now. If set to "none", only nodes frequencies can be output. @item asr.probabilities = @{boolean@} Tells if we should output the site specific probabilities in each case. @@ -1607,6 +1842,9 @@ @item output.nodes.file = @{@{path@}|none@} Ancestral nodes information: expected frequencies of ancestral states. +@item output.nodes.add_extant = @{boolean@} +Tell if leaf nodes should be added to the output file. + @end table @c ------------------------------------------------------------------------------------------------------------------ @@ -1756,7 +1994,7 @@ @c ------------------------------------------------------------------------------------------------------------------ -@node bppseqman, bpptreedraw, bppreroot, Reference +@node bppseqman, bppalnscore, bppreroot, Reference @section BppSeqMan: Bio++ Sequence Manipulation The Bio++ Sequence Manipulator convert between various file formats, and can also perform various operations on sequences. @@ -1807,6 +2045,9 @@ Change (partially) unresolved characters to gaps. @item RemoveStops +Remove all stop codons in sequences. If sequences are aligned, stop codons will be replaced by gaps. + +@item RemoveColumnsWithStops Remove all sites with at least one stop codon. @item GetCDS @@ -1826,6 +2067,13 @@ It is also possible to fix a maximum proportion of gaps, see specific options. @option{maxGapAllowed}: The maximum proportion of gaps allowed. +@item GetCodonPosition(position=@{1|2|3@}) +Retrieve the given positions from codon sequences (aligned or not). + +@item FilterFromTree(tree.file=@{path@}, tree.format=@{chars@}) +Get a subset of sequences based on a tree file. The order of sequences in the file will reflect the tree structure. All sequences which do not have a corresponding leaf in the tree, based on the sequence name, will be removed. +This method can therefore be used for subsetting a list of sequences, and/or rearrange them in a more convenient manner. + @end table Examples of use: @@ -1861,7 +2109,61 @@ @c ------------------------------------------------------------------------------------------------------------------ -@node bpptreedraw, , bppseqman, Reference +@node bppalnscore, bpptreedraw, bppseqman, Reference +@section BppAlnScore: Bio++ Alignment Scoring + +This program compares two alignments and computes column scores. +Scores are output to a text file, and/or can be used to generate +a site selection, to be output in a mase file. + +The two input alignments are specified using the input.sequences +procedures (@pxref{Sequences}), with suffixes ``.test'' for the +first one, and ``.ref'' for the second. Scores will be computed +for each column of the ``.test'' alignment. + +Two scores are computed, following work by Thompson (1999): +@table @emph +@item column score (CS) +is 1 if the column is found in the reference alignment, 0 otherwise. +@item sum-of-pairs score (SPS) +is the proportion of pairs of residues which are also aligned in +the reference alignment. +@end table + +Specific options: +@table @command + +@item output.scores = @{path@} +A text file where scores can be written, one row per column. +If set to 'none', no file will be produced. + +@item output.mase = @{path@} +If not 'none', a Mase alignment will be generated, as a copy +of the ``.test'' input alignment, with two sites selections +names CS and SPS. + +@item output.sps_thresholds = @{float@} +The threshold to use for generating the site selection based +on SPS score. All positions with at least the threshold value +will be included in the selection. + +@item score.word_size = @{int>0@} +If alignment is for a word alphabet (typically codons), the word +size can be specified in order to produce a compatible site selection. +Please note that in this case, the alignment must not be loaded with +the world alphabet, but the corresponding letter alphabet. + +@item score.phase = @{int>0|chars@} +Eather a number (1-based) stating the starting position for words, +or the starting word. In this latter case, the first occurrence of the +word in all sequences will be used to determine the phase. + +@end table + + +@c ------------------------------------------------------------------------------------------------------------------ + +@node bpptreedraw, , bppalnscore, Reference @section BppTreeDraw: Bio++ Tree Drawing This is a simple program that outputs a tree in various vector formats. diff -Nru bppsuite-0.6.2/doc/version.texi bppsuite-0.7.0/doc/version.texi --- bppsuite-0.6.2/doc/version.texi 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/doc/version.texi 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -@set VERSION 0.4 -@set UPDATED 1 diff -Nru bppsuite-0.6.2/Examples/AlignmentScoring/AlnScores.bpp bppsuite-0.7.0/Examples/AlignmentScoring/AlnScores.bpp --- bppsuite-0.6.2/Examples/AlignmentScoring/AlnScores.bpp 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/AlignmentScoring/AlnScores.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,13 @@ +DATA=HIV1_REF_2010_gag + +input.sequence.file.test = ../Data/$(DATA)_DNA.fasta +input.sequence.format.test = Fasta +input.sequence.file.ref = ../Data/$(DATA)_macse_DNA.fasta +input.sequence.format.ref = Fasta + +score.word_size = 3 +score.phase = ATG + +output.scores = $(DATA).scores.txt +output.mase = $(DATA).filter.mase +output.sps_thresholds = 0.8 diff -Nru bppsuite-0.6.2/Examples/Data/HIV1_REF_2010_gag_DNA.fasta bppsuite-0.7.0/Examples/Data/HIV1_REF_2010_gag_DNA.fasta --- bppsuite-0.6.2/Examples/Data/HIV1_REF_2010_gag_DNA.fasta 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/Data/HIV1_REF_2010_gag_DNA.fasta 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,1638 @@ +>Ref.A1.AU.03.PS1044_Day0.DQ676872 +ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAGATTAGATGCATGGGA +GAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATC +TAGTATGGGCAAGCAGGGAGCTGGAGAGATTCGCACTTAAYCCTRGCCTT +TTAGAATCAGCAGAAGGATGTCAACAAATAATGGAACAGTTACAACCAGC +TCTYAAGACAGGAWCAGAAGAAATTAAATCATTATTTAATACAGTAGCAA +CCCTCTATTGTGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCT +YTAGATAAAATAGAGGAAATAAAA------------AAT----------- +----------AAG---------------AGCAAG------CAAAGG---- +-----------------------------ACTCAACAGGCAGCAGCT--- +------------------------------GACACAGGA----------- +-------------------------------------------------- +-----------------------------AACAGCGGCAAG--------- +---------GTCAGCCAAAATTACCCTATAGTGCAAAATGCACAGGGGCA +AATGATACAYCAAAACTTGTCACCTAGAACTTTAAATGCATGGGTAAAAG +TAATAGAA---GAAAAGGCTTTTAGTCCAGAAGTGATACCCATGTTCTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATGTAATGCTGAACAT +AGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGACACCATCAATG +AAGAAGCTGCAGAATGGGACAGGTTACATCCAGTACATGCAGGGCCTATT +CCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGACATAGCAGGAGCTAC +TAGTACCCCTCAAGAACAATTACAATGGATGACA---------GGCAACC +CACCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTACTAGCATTTTGGATATAAG +ACAAGGGCCAAAAGAATCCTTCAGAGACTATGTAGATAGGTTCTTTAAAG +CTCTTAGAGCTGAGCAAGCTACACAGGAGGTAAAAAGTTGGATGACAGAG +ACATTACTGGTC---CAAAATGCAAATCCAGATTGTAAGTCCATTCTAAA +AGCATTAGGATCAGGAGCTACATTAGAAGAAATGATGACAGCATGCCAGG +GAGTGGGAGGACCCAGCCATAAGGCAAGGGTTTTGGCTGAAGCAATG--- +---------AGTCAAGCACAA------------------------CAAAC +AAGCATAATGATGCAGAGA---GGCAAC---TTTAGGGGCGGCCAGAAA- +--AGG---ATTAAGTGTTTTAACTGTGGCAAAGAAGGACACCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGAAGGAGGG +ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAGCAAG---------GGG--- +AGGCCAGGAAATTTCCCTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCG---GAGCTCTTT +GGGATGGGG---------------GAAGAGATA---ACCTCCCCT----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAGGACAAG---------------------GAACAGGTC--- +---CCACCC---TTA---GTTTCCCTCAAATCACTCTTTGGCAACGACCC +ATCGTCACAGTAA +>Ref.A1.RW.92.92RW008.AB253421 +ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGA +AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATC +TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTGGCCTT +TTAGAAACAACAGAAGGATGTCAAAAAATAATAGAACAGTTACAACCATC +TGTCAAGACAGGAACAGAAGAACTTAAATCATTATTTAATACAGTAGCAA +CCCTCTATTGCGTACATCAACGGATAGATGTAAAAGACACCAAGGAAGCC +CTAGATAAAATAGAGGAAATGCAA------------AAT----------- +----------AAG---------------AGCAAG------CAAAAG---- +-----------------------------ACACAACAGGCAGCAGCT--- +------------------------------GACATAGGA----------- +-------------------------------------------------- +-----------------------------AATAGCAGCAAG--------- +---------GTCAGCCAAAATTACCCTATAGTGCAAAATGCACAAGGGCA +AATGATATATCAGTCCATGTCACCTAGGACTTTGAATGCATGGGTGAAAG +TAATAGAA---GAAAAGGGTTTCAACCCAGAAGTAATACCCATGTTCTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATATGATGCTAAACAT +AGTGGGGGGACATCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGACTGGGACAGGTTACATCCAGTACAGGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCCTCAAGAACAAATAGGATGGATGACA---------AGCAACC +CACCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGATGTAAA +ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAA +TTCTCAGAGCTGAACAAGCTACACAGGATGTAAAACATTGGATGACAGAA +ACATTGCTGATC---CAAAATGCAAATCCAGATTGTAAGTCCATTTTAAG +AGCATTAGGAACAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTAGCTGAGGCAATG--- +---------AGTCAAGTACAA------------------------CATCC +AAACATAATGATGCAGAGA---GGCAAT---TTTAGGGGC---CAGAAA- +--AGG---ATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG +ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAGCAAG---------GGG--- +AGGCCAGGAAATTTTCCTCAGAGC-------------------------- +----AGACCG------GAGCCATCAGCC---------------------- +-----------------------------CCACCAGCA---GAGATCTTT +GGGATAGGG---------------GAAGAGATA---GCCTCCCCT----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGACAGG---------------------GAACCGGCC--- +---CAACCT---TTA---GTTTCCCTCAAATCACTCTTTGGCAACGACCC +CTTGTCACAGTAA +>Ref.A1.UG.92.92UG037.AB253429 +ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATC +TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTAGCCTT +TTAGAAACAACAGAAGGATGTCAACAAATAATGGAACAATTACAATCAGC +TCTCAGAACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAA +CCCTCTATTGCGTACATCAACGGATAGAGGTAAAAGACACCAAGGAAGCT +CTAGATAAAATAGAGGAGATACAA------------AAG----------- +----------AAA---------------AGCAAG------CAAAAG---- +-----------------------------ACACAGCAGGCAGCAGCT--- +------------------------------GACACAGGA----------- +-------------------------------------------------- +-----------------------------AGTAGCAGCAAG--------- +---------GTCAGCCAAAATTACCCTATAGTGCAAAATGCACAAGGGCA +AATGATCCACCAGTCCTTGTCACCTAGGACTTTGAATGCATGGGTGAAAG +TAATAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTCTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTGAATATGATGCTGAACAT +AGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGCTACATCCAGTACATGCAGGGCCTGTT +GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCCTCAAGAACAAATAGCATGGATGACA---------GGCAACC +CACCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTAGATATAAA +ACAAGGGCCAAAAGAACCCTTCAGAGACTATGTAGATAGGTTTTTTAAAA +CTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAGGTTGGATGACAGAA +ACATTACTGATC---CAAAATGCAAATCCAGATTGTAAATCCATCCTAAG +AGCATTAGGAGCAGGGGCTACATTAGAAGAAATGATGACAGCATGCCAGG +GAGTGGGAGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGTCAAGTACAA------------------------CATAC +AAACATAATGATGCAGAGA---GGCAAT---TTTAAGGGC---CAGAAA- +--AGG---ATTAAGTGTTTCAACTGTGGCAAAGAAGGACATCTAGCCAAA +AATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAGGGAAGG +GCACCAAATGAAGGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATCTGG---CCT---TCCAGCAAA---------GGG--- +AGGCCAGGAAATTTTCCTCAGAGC-------------------------- +----AGACCA------GAACCAACAGCC---------------------- +-----------------------------CCACCAGCAGCAGAGATCTTT +GGGATGAGG---------------GAAGAGATA---GTCTCCCCT----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AACGACAGG---------------------GACCAGAAC--- +---CCACCT---TCA---GTTTCCCTCAAATCACTCTTTGGCAACGACCT +CTTGTCACAGTAA +>Ref.A2.CD.97.97CDKTB48.AF286238 +ATGGGTGCGAGAGCGTCAGTATTGAGCGGCGGAAAATTAGAAGCTTGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATT +TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCTCAATCAACCCCAGCCTT +TTAGAAACAGAAACAGGATGTAGACGAATATTTGGGCAATTACAACCAGC +TCTCGAGACAGGAACAGAAGAACTTAGATCATTATATAATACAATAGCAG +TCCTCTACTTTGTTCATCAAAAGATAGAGGTAAAAGACACCAAGGAAGCT +CTAGATAAAATAGAGGAAGAACAA------------AAC----------- +----------AAA---------------TGCAAG------CAGAAG---- +-----------------------------ACACAGCAGGCAGCAGCT--- +------------------------------GACACAGGA----------- +-------------------------------------------------- +-----------------------------AGCAGCAGCAGTCAAAATTAC +AGAGGTAGCAGCAGTCAAAATTACCCTATAGTGCAAAATGCACAAGGGCA +AATGGTACACCAGGCCGTGTCACCTAGGACTTTGAATGCATGGGTCAAAG +TAGTTGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTACA +GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACAC +AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGTTACATCCAGTACAGGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCGGGAGCTAC +TAGTAACCTTCAGGAACAAATAGGATGGATGACC---------AGCAACC +CACCTATT---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAA +CTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGAC +ACCTTGCTGGTC---CAAAATGCAAACCCAGATTGTAAATCCATCTTGAG +GGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTAGCTGAAGCAATG--- +---------AGCCAAGTACAA------------------------AATAC +AAACATAATGATACAGAGA---GGCAAT---TTTAAGGGT---CAAAAA- +--AGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAATGTGGGAAGGAAGG +ACATCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAA---------GGG--- +AGGCCAGGGAATTTTCCTCAGAGC-------------------------- +----AGGACA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAATG------------ +------GAG---------------GAAGAGATA---ACCTCCTCG----- +-------------------CTGAAGCAGGAG------------------- +-----------AACAGG---------------------GAGCCGTCC--- +---ACCCCT---GCA---ATTTCCCTCAAATCACTCTTTGGCAACGACCT +CTTGTCACAGTGA +>Ref.A2.CM.01.01CM_1445MV.GU201516 +------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGAATGAAACATT +TAGTATGGGCAAGCAGGGAGCTGGAAAAATACTCAATCAACCCTGGTCTT +TTAGAAACATCGGAAGGATGTAAACAAATAATAAGGCAGTTACATTCAGC +TCTCCCAGTAGGAACAGAAGAACTTAAATCACTATATAATACAATAGCAG +TCCTCTACTATGTACATCAAAAAATAGAGGTAAAAGACACCAAGGAAGCC +CTAGATAAATTAGAGGAGGAGCAA------------AAC----------- +----------AAA---------------TACAAG------CAGAAG---- +-----------------------------ACACAGCAGGCAGCAGCT--- +------------------------------GCCACAGGA----------- +-------------------------------------------------- +-----------------------------AATAGCAGC------------ +------------AGTCAGAATTATCCCATAGTGCAAAATGCACAAGGGCA +AATGGTGCACCAGGCCATATCGCCTAGGACTTTGAATGCATGGGTCAAAG +TAGTAGAA---GAAAAAGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACTATGCTAAACAC +AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAGGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGGATGGATGACC---------AGCAACC +CACCTATC---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCCAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAA +CTCTCAGAGCTGAACAAGCTACACAGGATGTAAAAAATTGGATGACAGAC +ACCTTGCTGGTC---CAAAATGCGAACCCAGATTGTAAAACTATCCTGAG +AGCGTTAGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCGGCCATAAAGCAAGGGTCTTGGCTGAAGCAATG--- +---------AGCCAAATACACAGTACA------------------AATCA +AAATGTAATGATGCAGAGA---GGCAAT---TTTAGAGGT---CCAAAA- +--AGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGTTGCTGGAAATGTGGGAAGGAAGG +ACATCAAATGAAAGATTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATCTGG---CCT---CCCAACAAA---------GGG--- +AGGCCAGGAAACTTTCCCCAGAGC-------------------------- +----AGAACA------GAGCCAACAGCC---------------------- +-----------------------------CCGCCAGCA---GAGAACGTT +GGAATGGGG---------------GAAGAGATA---GCTTCCTCG----- +-------------------TCGAAGCAGGAACTG---------------- +--------AGAAACAGG---------------------GAACAACAC--- +---ACTCCT---ACA---ATTTCCCTCAGATCACTCTTTGGCAACGACCC +CTTGTCACAGTAA +>Ref.A2.CY.94.94CY017_41.AF286237 +ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGCTTGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATT +TGGTATGGGCAAGCAGGGAGCTGGAGAAATTCTCAATTAACCCTGGCCTT +TTAGAAACACCAGAGGGATGTAGACAAATAATAAGGCAGTTACAACCAGC +TCTCCAAACAGGAACAGAAGAACTTAAATCATTATATAATACAGTAGTAG +TCCTCTACTGGGTACATCAAAGGGTAGATGTAAAAGACACCAAGGAAGCT +CTAGATAAAATAGAGGAAGAACAA------------AAC----------- +----------AAG---------------------------CAGAAA---- +-----------------------------ACACAGCATGCAGCAGCT--- +------------------------------GACACAGGG----------- +-------------------------------------------------- +-----------------------------AACAGCAGC------------ +------------AGTCAAAATTATCCCATAGTGCAAAATGCACAAGGGCA +AATGGTACACCAGGCTATATCACCTAGGACGTTGAATGCCTGGGTCAAAG +TAGTAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCTATGTTTACA +GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACAC +AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGGTTGGATGACC---------AGCGATC +CACCCATC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGGTTCTTTAAAA +CTCTAAGAGCTGAGCAAGCCACACAGGAGGTAAAAAACTGGATGACGGAC +ACCTTGCTGGTC---CAAAATGCGAACCCAGATTGTAGATCCATCTTGAG +AGCATTAGGACCAGGGGCCTCATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTGGCTGAAGCAATG--- +---------AGCCATGTACAAAGTACA------------------AATAC +AAACATAATGATGCAGAGA---GGCAAT---TTTAGGGGT---CAAAAA- +--AGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAATGTGGAAAGGAAGG +ACATCAAATGAAAGATTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAA---------GGG--- +AGGCCAGGAAATTTTCCTCAGAGC-------------------------- +----AGAACA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAACTTG +AGAATGGGG---------------GAAGAGATA---ACCTCCTCC----- +-------------------CTGAAGCAGGAACTG---------------- +--------GAGACCAGG---------------------GAACCATAC--- +---AATCCT---GCA---ATTTCCCTCAAATCACTCTTTGGCAACGACCC +CTTGTTACAGTAA +>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGA +AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATA +TAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTG +TTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATC +CCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAA +CCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCT +TTAGACAAGATAGAGGAAGAGCAA------------AAC----------- +----------AAA---------------AGTAAG------AAAAAA---- +-----------------------------GCACAGCAAGCAGCAGCT--- +------------------------------GACACAGGA----------- +-------------------------------------------------- +-----------------------------CACAGCAATCAG--------- +---------GTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCA +AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAGTAGAA---GAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG +AGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATT +GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGGATGGATGACA---------AATAATC +CACCTATC---CCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAG +ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAA +CTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACTATTTTAAA +AGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATG--- +---------AGCCAAGTAACAAAT---------------------TCAGC +TACCATAATGATGCAGAGA---GGCAAT---TTTAGGAAC---CAAAGA- +--AAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGATTGTACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAGATCTGG---CCT---TCCTACAAG---------GGA--- +AGGCCAGGGAATTTTCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGAA---GAGAGCTTC +AGGTCTGGG---------------GTAGAGACAACAACTCCCCCT----- +-------------------CAGAAGCAGGAGCCG---------------- +--------ATAGACAAG---------------------GAACTGTAT--- +------CCT---TTA---ACTTCCCTCAGGTCACTCTTTGGCAACGACCC +CTCGTCACAATAA +>Ref.B.NL.00.671_00T36.AY423387 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATAGATGGGA +AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAGATATAAATTAAAACATA +TAGTATGGGCAAGCAGAGAGCTAGAACGATTCGCAGTTAATCCTGGCCTT +TTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCAGC +CCTTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAA +CCCTCTATTGTGTGCATGCAAGGATAGAGGTAAAAGACACCAAGGAAGCT +TTAGAAAAAATAGAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTAAG------AAACGG---- +--------------GCACAGCAA------GCACAGCAAGCAGAAGCT--- +------------------------------GACGCAGGA----------- +-------------------------------------------------- +-----------------------------AAAAACAACCCG--------- +---------GTCAGCCAGAATTACCCTATAGTGCAGAATCTCCAAGGGCA +AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAGTAGAA---GAGAAGGCCTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG +AGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCCGGGCCTATT +GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGGATGGATGACA---------AATAATC +CACCTATC---CCAGTAGGAGAAATATATAAGAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAA +ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAA +CTTTAAGAGCTGAGCAAGCCTCACAGGAAGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAATTCGAACCCAGATTGTAAAACTATTTTAAA +AGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACCGCATGTCAGG +GAGTAGGGGGACCCGGCCATAAAGCGAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGTAACAAGT---------------------GCACC +TGCCATAATGATGCAGAGA---GGCAAT---CATAGAAAC---CAAAGA- +--AGGACTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAGA +AATTGCAGGGCCCCTAGNAAAAAGGGCTGTTGGAAATGTGNAAAGNAAGG +ACACCAAATGAAAGATTGTACT---------NAG---AGACAGGCTANTT +TTTTAGGGAAGATTTGG---CCT---TCCCACAAG---------GGG--- +AGGCCAGGGAATTTTCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC----------------CCTTCT +CAGAGCAGACCAGAGCCAAC---AGCC--CCACCAGAA---GAGAGCTTC +AGGTTTGGG---------------GAAGAGACAACAACTCCCTCT----- +-------------------CAGAGGCAGGAGCCA---------------- +--------ACAGACAAG---------------------GAACTGTAT--- +------CCT---TTA---GCTTCCCTCAAATCACTCTTTGGCAGCGACCC +ATAGTCACAATAA +>Ref.B.TH.90.BK132.AY173951 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATAGATGGGA +GAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATA +TAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTA +TTGGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCAAG +CCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAG +TCCTCTATTGTGTACATCAAAAGATAGAGGTAAAAGACACCAAGGAAGCT +TTAGAGAAGATAGAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTAAG------AAAAAG---- +-----------------------------GCACAGCAAGCAGCAGCT--- +------------------------------AACACAGAA----------- +-------------------------------------------------- +-----------------------------AACAGCAGCCAG--------- +---------GTTAGCCAAAATTACCCTATAGTGCAAAATATGCAGGGGCA +AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAGTAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG +AGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATT +GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGGATGGATGACA---------CATAATC +CACCTATC---CCAGTGGGAGAAATTTACAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGGATGTATAGCCCTACCAGCATTTTGGACATAAG +ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAGA +CTCTAAGAGCCGAGCAAGCCTCACAGGAGGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACTATTTTAAA +AGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGTCCCGGCCATAAGGCAAGAGTTTTGGCGGAAGCAATG--- +---------AGCCAAGTGACAAAT---------------------TCAGC +TACCATAATGATGCAGAAA---GGCAAT---TTTAGGAAC---CAAAGA- +--AAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCCGA +AATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAGATGTGGAAAGGAAGG +ACACCAAATGAAAGATTGTACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATCTGG---CCT---TCCCACAAG---------GGA--- +AGGCCAGGGAATTTTCTTCAGAGC-------------------------- +----AGACCA------GAGCCGACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +AGGTTTGGG---------------GAAGAGACAACAACTCCCTCT----- +-------------------CAGAAGCAGGAGACA---------------- +--------ATAGACAAG---------------------GAACTATAT--- +------CCT---TTA---ACTGCCCTCAAATCACTCTTTGGCAACGACCC +CTCGTCACAATAA +>Ref.B.US.98.1058_11.AY331295 +------------GCGTCAGTATTAAGCGGGGGAAAATTAGATACATGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATA +TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTGGCCTG +TTAGAAACAGCAGAAGGCTGTAGACAATTATTGGGACAGCTACAGCCATC +CCTTCAAACAGGATCAGAAGAACTTAAATCATTATTTAATACAATAGCAA +CCCTCTATTGTGTACATCAAAGGATAGAGGTAAGAGACACCAAAGAGGCT +TTAGACAAGATAGAGGAAGAGCAA------------AAC----------- +----------AAA---------------AGTAAG------AAAAAA---- +-----------------------------GCACAGCAAGCAGCAGCT--- +------------------------GCAGCTGACACAGGA----------- +-------------------------------------------------- +-----------------------------AACAGCAGCCAG--------- +---------GTCAGCCAAAATTACCCTATAGTGCAGAACCTCCAAGGGCA +AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAATAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTGCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAAACCATCAATG +AGGAAGCTGCAGAATGGGATAGAATACATCCAGCGCAAGCAGGGCCTATA +GCACCAGGCCAGATAAGAGACCCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAACATGGATGACA---------AATAATC +CACCTATC---CCAGTAGGAGAAATCTATAAAAAATGGATAATCATGGGA +TTAAATAAAATAGTAAGGATGTATAGTCCTACCAGCATTCTGGACATAAG +ACAAGGACCAAAGGAACCCTTTAGGGACTATGTAGACCGGTTCTATAAAA +CTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAACGCGAACCCAGATTGTAAGACTATATTAAA +AGCATTAGGACCAGCAGCTACACTAGAGGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATG--- +---------AGCCAAGTAACAAAT---------------------TCAGG +TGCCATAATGATGCAGAAA---GGCAAT---TTTAGGAAC---CAG---- +-----GTTGTTAGGTGTTTCAATTGTGGCAAAGTAGGGCACATAGCCAAA +AATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAAATGTGGAAAAGAAGG +ACACCAAATGAAAGATTGTGAT---------CAG---AGACAGGCTAATT +TTTTAGGGAAGATCTGG---CCT---TCCCACAAA---------GGA--- +AGGCCAGGGAATTTTCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +AGGTTTGGG---------------GAGGAGACAACAACTCCCTCT----- +-------------------CAGAAGCAGGAGCCA---------------- +--------CAAGAA------------------------TAT--------- +------CCT---TTA---GCTTCCCTCAGATCACTCTTTGGCAACGACCC +CTCGTCACAATAA +>Ref.C.BR.92.BR025_d.U52953 +ATGGGTGCGAGAGCGTCAATATTAAGAGGCGGAAAATTAGATGCTTGGGA +AAGAATTAAGTTAAAGCCAGGGGGAAAGAAACACTATATGATGAAACACC +TAGTCTGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTGACCCTGGCCTT +TTAGAGACATCCGAAGGCTGTAAACAAATAATGAAACAGCTACAACCAGC +TCTTCAGACAGGAACAAAGGAACTTATATCATTACATAATACGGTTGCAA +CTCTCTATTGTGTACATGAAAAGATAGATGTACGAGACACCAAGGAAGCC +TTAGACAAAATAAAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTCAG------CAAAAA---- +-----------------------------ACACAGCAGGCAGAAGCG--- +---------------------------GCTGACAAAGGA----------- +-------------------------------------------------- +--------------------------------------AAG--------- +---------GTCAGTCAAAATTATCCTATAGTACAGAATCTCCAAGGGCA +AATGGTACACCAGCCCATATCAGCTAGAACTTTGAATGCGTGGGTAAAGG +TAGTAGAG---GAGAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGTTAAATAC +AGTGGGGGGACACCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG +AGGAGGCTGCAGAATGGGATAGATTACATCCAGTGCATGCAGGGCCTGTC +GCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +CAGTACCCTTCAGGAACAAATAACATGGATGACA---------AATAACC +CACCTGTC---CCAGTAGGAGACATCTATAAAAGATGGATAATTCTGGGG +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAA +CTCTAAGAGCAGAGCAAGCTACCCAAGATGTAAAAAATTGGATGACAGAT +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAG +AGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGCCACAAAGCAAGAGTGTTGGCTGAGGCAATG--- +---------AGCAAAGTAAAC------------------------AATAC +AAACATAATGATGCAAAGA---AGCAAT---TGTAAAGGC---CCTAAA- +--AGAACTATTAAATGCTTCAACTGTGGCAAGGAAGGGCACTTAGCCAGA +AATTGCAGGGCTCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAAGAAGG +ACACCAAGTGAAAGACTGTACT---------GAG---AGGCAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCCACAGG---------GGG--- +AGGCCAGGAAATCTTCTTCAGAAC-------------------------- +----AGAACA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGAA---GAGAGCTTC +AGGTTTGGG---------------GAAGAGACAACAACTCCCTCT----- +-------------------CGGAAGCAGGAGACG---------------- +--------ATAGACAAG---------------------GAACTG------ +------CCC---TTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC +CTTGTCAACATAA +>Ref.C.ET.86.ETH2220.U46016 +ATGGGTGCGAGAGCGTCAATATTAAGAGGCGAAAAATTAGATGCCTGGGA +AAAAATTAAGTTAAGGCCAGGGGGAAAGAAACACTATATGCTGAAACACC +TAGTCTGGGCAAACAGGGAGCTGGAAAAATTTGCACTTAACCCTGACCTT +TTAGATACATCAGCAGGCTGTAAACAAATAATTAAACAGCTACAACCAGC +TCTTCAGACAGGAACAGAGGAACTTAAATCATTATTTAATACAGTGGCAA +CTCTCTATTGTGTACATCAAAAGATAGAGATAAAAGACACCAAGGAAGCC +TTAGACAAGATAGAGGAAGAACAA------------AAC----------- +----------GAA---------------AGTCAG------CAAAAA---- +-----------------------------ACACAGCAGGCAGGAGCA--- +---------------------------GCTGACAGAGGA----------- +-------------------------------------------------- +--------------------------------------AAG--------- +---------GACAGTCAAAATTATCCTATAGTGCAGAATATGCAGGGGCA +AATGGTACATCAGCCCATATCAGCTAGAACTTTGAATGCATGGGTAAAAG +TAGTAGAG---GAAAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACA +GCTTTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG +AGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTGTT +GCACCAGGCCAAATGAGAGACCCAAGGGGAAGTGACATAGCAGGAACAAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------GGGAACC +CACCTGTT---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGG +CTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTTTAAAA +CCTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAAACCATTTTAAG +AGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGCCCACAAAGCAAGAGTGTTGGCTGAGGCAATG--- +---------AGCCAAGTAAAC------------------------AATAC +AACCATAATGATGCAGAAA---AGCAAT---TTTAAGGGC---CCTAAA- +--AGAGCAATTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGTACC---------GAG---AGACAGGCTAATT +TTTTAGGGAGACTTTGG---CCT---TCCAACAAG---------GGA--- +AGGCCAGGGAATTTCCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---CCACCAGAGAGTCT----- +-----CAGACCAGAGCCAAC---AGCC--CCACCACCA---GAGAGCTTC +AGGTTCGAG---------------GAA---GCA---ACACCTTCT----- +-------------------CCGAAGCAGGAGCTG---------------- +--------AAAGACAGG---------------------GAA--------- +------GCC---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCA +CTTGTTACAATAA +>Ref.C.IN.95.95IN21068.AF067155 +ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATAAATGGGA +AAAAATTAGGTTAAGGCCAGGGGGAAAGAAACGCTATATGCTAAAACACC +TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCAGTTAACCCTGGCCTT +TTAGAGACAGCAGAAGGCTGTAAACAAATAATAAAACAGCTACAACCAGC +TCTTCAGACAGGAACAGAGGAACTTAGATCATTATTCAACACAGTAGCAA +CTCTCTATTGTGTACATGCAGGGATAGAAGTACGAGACACCAAAGAAGCC +TTAGACAAGATAGAAGAAGAACAA------------AAC----------- +----------AAA---------------ATTAAG------CAAAAA---- +-----------------------------ACACAGCAGGCAAAAGAG--- +---------------------------GATGAC---GGG----------- +-------------------------------------------------- +--------------------------------------AAG--------- +---------GTCAGTCAAAATTATCCTATAGTGCAGAATCTCCAAGGGCA +AATGGTACACCAAGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAG +TAATAGAG---GAAAAGGCTTTTAGCCCAGAGGTAATACCCATGTTTACA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGTTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG +AAGAGGCTGCAGAATGGGATAGATTACATCCAGTACCTGCAGGGCCTATT +GCACCAGGCCAACTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACG---------AATAACC +CACCTGTT---CCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGG +TTAAATAAAATAGTAAGAATGTATAGCCCTGTGAGCATTTTGGACATAAG +ACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAA +CTTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGTAAGACCATTTTAAG +AGCATTAGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGG +GAGTGGGAGGACCTAGCCACAAAGCAAGAGTGTTGGCTGAGGCAATG--- +---------AGCCAAACAAAC---------------------------AG +TGCCATACTGATGCAAAGA---AGCAAT---TTTAAAGGC---TCTAAA- +--AGAATTGTTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGTACT---------GAA---AGGCAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCCACAAG---------GGG--- +AGGCCAGGGAATTTCCTCCAGAGT-------------------------- +----AGACCA------GAGCCAACAGCT---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +AGGTTCGAG---------------GAG---ACA---ACCCCAGCT----- +-------------------CCGAAGCAGGAGCCG---------------- +--------AAAGACAGG---------------------GAA--------- +------CCT---TTA---ACTTCCCTCAGATCACTCTTTGGCAGCGACCC +CTTGTCTCAATAA +>Ref.C.ZA.04.04ZASK146.AY772699 +ATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGA +AAAAATTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACA +TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTCAACCCTGGCCTT +TTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAACCAGC +TATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAG +TTCTCTATTGTGTACATAAAAAGATAGATGTAAGAGACACCAAGGAAGCC +TTAGACAAGATAGAGGAAGAGCAA------------AAC----------- +----------AAA---------------AGTCAG------CAAAAA---- +-----------------------------ACACAGCAGGCAAAAGCG--- +---------------------------GCTGAC---GAA----------- +-------------------------------------------------- +--------------------------------------AAG--------- +---------GTCAGTCAAAATTTTCCTATAGTACAGAATCTTCAAGGGCA +AATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAG +TAATAGAG---GAGAAGGGTTTTAACCCAGAGGTAATACCCATGTTTACA +GCATTATCAGAGGGAGCCACCCCACAAGATTTGAACACCATGCTAAATAC +GGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATG +AAGAGGCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTC +GCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC +TAGTAACCTTCAGGAACAAGTAGCATGGATGACA---------AGTAACC +CACCTATT---CCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGA +TTAAATAAAATAGTGAGGATGTATAGCCCGGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAA +CTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAG +AGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAGCATGTCAAG +GGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATG--- +---------AGCCAAATAAAC------------------------AATGG +AAACATAATGATGCAGAGA---AGTAAT---TTTAAAGGC---CCTAAA- +--AGAATTGTTAAATGTTTTAACTGTGGCAAGGGGAGGCACATAGCCAAA +AATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGTACT---------GAA---AGGCAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCCAGAAG---------GGG--- +AGGCCAGGGAATTTTCTCCAGAAC-------------------------- +----AGACTA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +AGGTTCGAG---------------GAG---ACG---ACCCCTGCT----- +-------------------CCGAAACAGGAGCTG---------------- +--------AAAGACAGG---------------------GAA--------- +------CCT---TTA---ACTTCCCTCAGATCACTCTTTGGCAGCGACCC +CTTGTCTCAATAA +>Ref.D.CD.83.ELI.K03454 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATAAATGGGA +AAAAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAGACTAAAACATA +TAGTATGGGCAAGCAGGGAGCTAGAACGATATGCACTTAATCCTGGCCTT +TTAGAAACATCAGAAGGCTGTAAACAAATAATAGGGCAGCTACAACCAGC +TATTCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAA +CCCTCTATTGTGTACATAAAGGAATAGATGTAAAAGACACCAAGGAAGCT +TTAGAAAAGATGGAGGAAGAGCAA------------AAC----------- +----------AAA---------------AGTAAG------AAAAAG---- +-----------------------------GCACAGCAAGCAGCAGCT--- +------------------------------GACACAGGA----------- +-------------------------------------------------- +-----------------------------AACAACAGCCAG--------- +---------GTCAGCCAAAATTATCCTATAGTGCAGAACCTACAGGGGCA +AATGGTACATCAGGCCATATCACCTAGAACTTTGAACGCATGGGTAAAAG +TAATAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGCTAAAAGAGACCATCAATG +AAGAAGCTGCAGAATGGGATAGGTTACATCCAGTGCATGCAGGGCCTATT +GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AGTAACC +CACCTATC---CCAGTAGGAGAAATCTATAAAAGATGGATAATTGTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAGGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTATAAAA +CTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAATGCAAACCCAGATTGCAAGACTATCTTAAA +AGCATTGGGACCACAGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGGGGGCCCAGCCATAAAGCAAGAGTTCTGGCTGAGGCAATG--- +---------AGCCAAGCAACAAATTCA------------------GTTAC +TACAGCAATGATGCAGAGA---GGCAAT---TTTAAGGGC---CCAAGA- +--AAAATTATTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCAAAA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAGATGTGGAAAGGAAGG +ACACCAACTAAAAGATTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAGAATTTGG---CCT---TCCCACAAG---------GGA--- +AGGCCGGGGAACTTTCTCCAAAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTTGGG---------------GAAGAGATA---ACCCCCTCT----- +-------------------CAAAAACAGGAGCAG---------------- +--------AAAGACAAG---------------------GAACTGTAT--- +------CCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCC +CTTGTCGCAATAA +>Ref.D.CM.01.01CM_4412HAL.AY371157 +------GCGAGAGCGTCAATATTAAGCGGGGGAAAATTGGATGCATGGGA +AAAAATTCGGTTACGGCCAGGGGGAAGCAAAAAGTATAGGCTAAAACATC +TAATATGGGCAAGCAATGAGCTAGAACGATTTGCACTTAATCCTGGCCTT +TTAGAGACATCAGATGGCTGTAAACAAATACTAGGCCAGCTACAACCAGC +TCTTAAAACAGGAACAGAAGAACTTAGATCATTATTTAATGCAGTAGCAG +TACTCTATTGTGTACATGAAAGGATAGAGGTAAAGGACACCAAGGAAGCC +TTAGACAAGATAGAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTAAG------AAAAAA---- +-----------------------------GCACAGCAAGCAGCAGCT--- +------------------------------GACACAGGG----------- +-------------------------------------------------- +-----------------------------GACAACAAACAG--------- +---------GTCAGCCAAAATTATCCTATAGTGCAGAACTTACAGGGGCA +AATGGTACACCAAGCCCTATCACCCAGAACCTTGAACGCATGGGTAAAAG +TAATAGAG---GAAAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAGGATTTAAATACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG +AGGAAGCTGCAGAATGGGACAGGCTACATCCAGTGCAAGCAGGGCCTGTT +GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATTGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGGGTGGATGACA---------AGTAATC +CACCAATC---CCAGTAGGGGAAATCTATAAAAGATGGATAATCTTGGGA +TTGAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAG +ACAAGGACCAAAAGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAA +CTCTAAGAGCCGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGAA +ACCTTGTTGGTT---CAAAATGCAAACCCAGACTGTAAAACTATCTTAAA +GGCGTTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGGCCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGCAACAGCAGGT------------ATG---AATGC +TGCAATAATGATGCAGAGG---GGCAAT---TTTAAGGGC---CCAAAG- +--AGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGGCACATAGCAAAA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAGAGAAGG +ACACCAAATGAAAGATTGCACA---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGA--- +AGGCCAGGGAACTTTCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCGGG---------------GAGGAGATA---GCCCCCTCT----- +-------------------CAGAAACAGGAGCAG---------------- +--------AAAGACAAAGACCAG---------------GAACTGTAT--- +------CCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCC +CTTGTCACAATAA +>Ref.D.TZ.01.A280.AY253311 +------GCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATGCATGGGA +AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAACTAAAACATA +TAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCACTTAATCCTGGCCTT +TTAGAGACATCCGAAGGCTGTAAACAAAT----------CTACAACCAGC +TATTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAA +CCCTCTATTGTGTGCATAGAAAGATAGAGGTAAAAGACACCAAGGAAGCT +TTAGAAAAATTAGAGGAAGAGCAA------------ACC----------- +----------AAA---------------AGTAAG------AAAAAG---- +-----------------------------GCACAGCAAGCAACAGCT--- +------------------------------GACACAGGA----------- +-------------------------------------------------- +-----------------------------AGCAGCAGCCAG--------- +---------GTCAGCCAAAATTATCCTATAGTGCAAAACCTACAGGGGCA +AATGGTACACCAGGCCATATCACCTAGAACCTTGAACGCATGGGTAAAAG +TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACAATGCTAAACAC +AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGAGACCATCAATG +AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATT +GCACCAGGACAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AATAATC +CACCTGTC---CCAGTAGGAGAAATATATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAG +ACAAGGACCAAAGGAGCCCTTTAGGGACTATGTAGATCGGTTCTATAAAA +CTCTAAGAGCCGAGCAAGCTTCACAAGATGTAAAAAATTGGATGACTGAA +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAAACTATCTTAAA +AGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGGGGACCCAGTCATAAGGCAAGAGTTCTAGCTGAGGCAATG--- +---------AGCCAAGCAACAAATGTA------------------AATGC +TGCCATAATGATGCAGAGA---GGTAAT---TTTAAGGGC---CCAAGG- +--AAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGACACATAGCAAAA +AATTGCAGGGCCCCAAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGATTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCCACAAA---------GGA--- +AGGCCAGGGAACTTCCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGATCTTC +GGGTTTGGG---------------GAGGAGATA---AAACCCTCT----- +-------------------CAGAAACAGGAGCAG---------------- +--------AAAGACAAG------------GACAAG---GAACTGTAT--- +------CCT---TCA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC +CTTGTCACAATAA +>Ref.D.UG.94.94UG114.U88824 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGAGGAAAATTAGATGAATGGGA +AAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATC +TAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCACTTAATCCTGGCCTT +TTAGAAACATCAGAAGGCTGTAGACAAATAATAAGACAGCTACAACCATC +TATTCAGACAGGATCAGAGGAAATTAAATCATTATATAATACAGTGGTAA +CCCTCTATTGTGTACATGAGAGGATAAAGGTAGCAAGCACCAAGGAAGCT +TTAGACAAGATAGAGGAAGAACAA------------GCC----------- +----------AAA---------------AGTAAG------AAAAAA---- +-----------------------------GCACAGCAAGCAACAGCT--- +------------------------------GACACAAGA----------- +-------------------------------------------------- +-----------------------------AACAGCAGCCAG--------- +---------GTCAGCCAAAATTATCCTATAGTGCAAAACCTACAGGGGCA +AATGGTACACCATCCCCTATCACCTAGAACTTTGAACGCATGGGTAAAAG +TAATAGAG---GAGAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAGGATACCATCAATG +AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTGTT +GCACCAGGCCAATTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTAACCTTCAGGAACAAATAGGATGGATGACA---------AGCAATC +CACCTATC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAA +CTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACTGAA +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAAACTATCTTAAA +AGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGGGGACCCAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGCAACAAATGCA------------------AATAC +TGCTATAATGATGCAGAGA---GGCAAT---TTTAAGGGC---CCAAAG- +--AAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGGCACACGGCAAAA +AATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAGGGAAGG +ACACCAAATGAAAGATTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCCACAAT---------GGA--- +AGGCCAGGGAATTTCCTTCAGAGC-------------------------- +----AGACCCCCAGCAGAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGATCTTC +GGATTAGGG---------------GAGGAGATA---ACACCTCCT----- +-------------------CAGAAACAGGAGCAG---------------- +--------AAAGACAAG---------------------GAACTGTAT--- +------CCT---TTA---ACCTCCCTCAAATCACTCTTTGGCAACGACCC +GTTGTCACAGTAA +>Ref.F1.BE.93.VI850.AF077336 +ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGAATGGGA +AAAAATTCAGTTAAGGCCGGGGGGAAAGAAAAGATATAAAATGAAACATC +TAATATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCTGGCCTT +CTAGAAACATCAGAAGGCTGTCAAAAAATAATAAGACAGCTACAACCATC +CCTTCAGACAGGATCAGAAGAGCTTAAGTCATTATTTAATACAGTAGCAG +TCCTCTATTATGTACATCAAAGGGCAGGGGTAACAGACACCAAGGAAGCT +TTAGACAAGCTAGAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTCAG------CAAAAG---- +-----------------------------ACACAGCAAGCGGCAGCT--- +------------------------------GACAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA +AATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAGG +TGATAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGGGCCACTCCCACAGATTTAAACACCATGCTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG +AGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGGCCTGCC +CCACCAGGCCAGATGAGGGAACCTAGGGGGAGTGATATAGCTGGAACTAC +TAGTACCCTTCAGGAACAAATACAATGGATGACG---------GGCAACC +CACCTGTC---CCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGATTCTTTAAAG +TCCTAAGAGCTGAGCAAGCTTCACAGGACGTAAAGGGTTGGATGACAGAC +ACATTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA +AGCATTGGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCCGAGGCAATG--- +---------AGTCAAGCAAAT---------------------------TC +AGCCATAATGATGCAGAAA---AGTAAT---TTTAAGGGC---CAAAGA- +--AGAGTTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAGAGAAGG +ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCCGGAAATTTCCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCAGA---------------GAGGAGATA---ACCCCCTCT----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGACGGG---------------------GAACTGTAC--- +---CCTCCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC +TTAGTCACAATAA +>Ref.F1.BR.93.93BR020_1.AF005494 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA +AAAAATTCGGTTAAGGCCGGGGGGAAAGAAAAAATATAGACTAAAACATC +TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCAGGCCTT +CTAGAAACATCAGAAGGCTGTCGAAAAATAATAGGACAGTTACAACCATC +CCTTCAGACAGGATCAGAAGAGCTCAAATCATTATATAATACAATAGCAG +TCCTCTATTATGTACATCAAAAGGTAGAGGTAAAAGACACCAAGGAGGCT +TTAGAGAAGCTAGAGGAAGAACAA------------AAC----------- +----------AAA---------------GGTCGG------CAAAAG---- +-----------------------------ACACAGCAAGCGACTGCT--- +------------------------------GAAAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA +AATGGTACACCAGTCTTTATCACCTAGAACTTTAAATGCATGGGTAAAGG +TGATAGAA---GAGAAGGCTTTTAGTCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGTTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG +AGGAGGCTGCAGAATGGGACAGATTACATCCAACACAGGCAGGACCCATC +CCCCCAGGTCAGATAAGGGAACCTAGGGGAAGTGATATAGCTGGAACTAC +TAGTACCCTTCAGGAACAAATACAATGGATGACA---------GGCAACC +CACCTGTC---CCAGTGGGAGAAATGTATAAAAGATGGATCATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCGGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA +CCCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA +AGCATTGGGACCAGGGGCTACACTAGAGGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGCAACA------------------------AATAC +AGCTATAATGATGCAGAAA---AGTAAC---TTTAAGGGC---CAAAGA- +--AGAATTGTTAAATGCTTTAATTGTGGCAAAGAAGGACACATAGCCAAA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAGTGTGGAAGAGAGGG +ACACCAAATGAAGGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCCGGAAACTTCATCCAGAAC-------------------------- +----AGGCCA------GAGCCGTCAGCC---------------------- +-----------------------------CCGCCAGCA---GAGAGCTTC +AGGTTCGGG---------------GAGGAGACA---ACCCCATCT----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGACGAG---------------------GGACTGTAC--- +---CCTCCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC +CTAGTCACAATAA +>Ref.F1.FI.93.FIN9363.AF075703 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAACTAGATGCATGGGA +AAAAATTCGGTTAAGGCCGGGGGGAAAGAAACAATATAGAATAAAACATC +TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCAATAGATCCTGGCCTT +CTAGAAACATCAGAAGGCTGTCAAAAAATAATAGCACAGATACAGCCATC +CATTCAGACAGGATCAGAAGAGCTTAGATCATTATATAACACAATAGCAG +TCCTCTATTTTGTACATCAAAAGATAGAGGTAAAGGACACCAAGGAAGCT +TTAGATAAGCTAGAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTCAG------CAAAAG---- +-----------------------------ACACAGCAAGCGGCAGCT--- +------------------------GCAGCTGACAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA +AATGGTACATCAGGCTATATCACCTAGAACTTTAAATGCATGGGTAAAGG +TGATAGAA---GAGAAGGCTTTTAGCCCAGAAGTTATACCCATGTTTTCA +GCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGCTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATTAATG +AGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGACCTATT +CCACCAGGCCAGATGAGGGAACCTAGGGGAAGCGATATAGCTGGAACTAC +TAGTACCCTTCAGGAACAAATACAATGGATGACA---------AGTAACC +CACCTGTC---CCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGA +TTAAATAAAATAGTAAGGATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAG +CTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGTAAGATCATTTTAAA +AGGATTGGGAATAGGGGCTACACTAGAAGAAATGATGACAGCATGTCGGG +GAGTGGGAGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATG--- +---------AGCCAAGCAAAT---------------------------AC +AACCATAATGATGCAGAAA---AGTAAT---TTTAGGGGC---CAAAGA- +--AGAATTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGA +AATTGCAGGGCCCCCAGGAAAAAGGGCTGTTGGAAATGTGGACAAGAAGG +GCACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCCGGAAATTTCCTTCAGAGT-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCGCCAGCA---GAGAGCCTC +GGGATCAGA---------------GAAGAGGTA---ACTCCCTCT----- +-------------------CCGAGGCAGGAGCAG---------------- +--------AAAGAAGAG---------------------GGACAGTAC--- +---CCTCCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC +CTAGTCACAATAA +>Ref.F1.FR.96.96FR_MP411.AJ249238 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA +AAGAATTCGATTAAGACCGGGGGGAAAGAAAAAATATAGAATGAAGCATC +TAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCAGTTGATCCTGGACTT +CTAGAAACACCAGAAGGCTGTAAGCAAATAATAAGACAGCTACAACCATC +CCTTCAGACAGGATCAGAAGAGCTTAGATCATTGTTCAATACAGTAGCAG +TTCTCTATTGTGTACATCAAAAGATAGAGATAAAGGACACCAAGGAAGCT +TTAGAGAAGTTAGAGGAGGAACAA------------AAC----------- +----------AAA---------------GGTCAG------CAAAAG---- +-----------------------------ACACAGCAAGCGGCAGCT--- +------------------------------GACAAAGGA----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAAAATCTTCAGGGACA +GATGGTACATCAGCCTATATCACCTAGAACTTTAAATGCATGGGTAAAAG +TGATAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTCTCA +GCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAATAC +AGTGGGTGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG +AGGAAGCTGCAGAATGGGACAGATTACATCCAGCGCATGCAGGGCCTATC +CTACCAGGCCAGATGAGAGAACCTAGGGGTAGTGACATAGCTGGAACTAC +TAGTACCCTTCAGGAACAAATACAATGGATGACA---------AGCAACC +CACCTGTC---CCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAG +ACAAGGGCCAAAGGAACCTTTTAGAGACTATGTGGACAGGTTCTTTAAAA +CTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAGAATTGGATGACAGAA +AGCTTGCTGGTG---CAAAATTCGAACCCAGACTGTAAGACCATCTTAAA +AGCATTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGCCATAAGGCAAGGGTTTTGGCTGAGGCCATG--- +---------AGCCAAGCAACA------------------------AATGC +AGCTATAATGATGCAGAAA---AGTAAC---TATAAGGGC---CCAAGA- +--AGATTTATTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAAA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAAGAAGG +ACATCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCCGGAAATTTTCTTCAGAAC-------------------------- +----AGGCCA------GAGCCAACAGCC---------------------- +-----------------------------CCGCCAGCG---GAGAGCTTC +GGGTTCAAA---------------GAGGAAATA---ACCCCCTCT----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAGGACGAG------------GGACAG---GGACTGTAT--- +---CCTCCC---TTA---GCCTCCCTCAAATCACTTTTTGGCAGCGACCC +TTAGTCACCATAA +>Ref.F2.CM.02.02CM_0016BBY.AY371158 +------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGACTGGGA +GAAAATTCGGTTAAGGCCGGGAGGGAAGAAAAAATATAGGCTAAAACATA +TAGTATGGGCAAGCAAGGAGCTAGAACGATTTGCACTTAATCCTGGCCTT +TTAGAGACAACAGAAGGCTGTAAACAAATAATAGGACAACTACAATCATC +CCTTCAGACAGGATCAGAAGAGATTAAATCATTATATAACACAGTAGCAG +TCCTCTATTATGTACATCAAAAGATACAAATAAGAGACACCAAGGAAGCT +TTAGATAAGCTACAGGAAGAACAA------------GAC----------- +----------AAA---------------TATCAG------CAAAAA---- +-----------------------------ACACAACCAGCAGCGGCT--- +------------------------------GATAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGGCA +AATGGTACATCAGGCTATATCACCTAGAACTCTAAATGCATGGGTAAAAG +TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTCATACCCATGTTTTCA +GCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTAGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCAGGCAGGACCTATC +CCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AGCAACC +CACCTGTC---CCAGTAGGAGAAATTTATAAAAGATGGATAATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA +CTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA +AGCACTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGCCATAAAGCAAGAATTTTGGCTGAGGCAATG--- +---------AGCCAAGTAACA------------------------GCTAC +ATCCGTACTGATGCAGAAA---AGCAAC---TTTAAGGGC---CAAAAA- +--AGAATTGTCAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAA +AATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAA---------GGG--- +AGGCCTGGGAATTTCATTCAGAGC-------------------------- +----AGACCA------GAGCCAACGGCC---------------------- +-----------------------------CCGCCAGCA---GAGGGCTTC +GGGTTCGGA---------------GAAGAGATA---ACTCCCTCC----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGACAAG---------------------GGACTGTAT--- +---CCTCCC---TTG---ACTTCCCTCAAATCACTCTTTGGCAACGACCC +GTAGTCACAATAA +>Ref.F2.CM.95.95CM_MP255.AJ249236 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA +AAAAATTCGGTTAAAGCCGGGGGGAAAGAAAAGATATAGGCTAAAACATC +TAGTATGGGCAAGCAGGGAACTAGAACGATTTGCACTTAATCCTAGCCTT +TTAGAAACAACAGAAGGCTGTAAGAAAATAATAGGACAATTACAATCATC +CCTTCAGACAGGATCAGAAGAGCTTAAATCACTATACAATGCAGTAGTAG +TTCTCTATTATGTACATCAAAGGATAGATGTAAGAGACACCAAGGAAGCT +TTAGATAAGCTACAGGAAGAACAA------------GAT----------- +----------AAA---------------AGTCAG------CAAAAG---- +-----------------------------GAACAACAAAAGGCGGCT--- +------------------------------GACAAAGAG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTGCAGAATATTCAGGGGCA +AATGGTACACCAGGCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAATAGAA---GAGAAGGCTTTCAGTCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGGGCCACCCCACAAGATTTAAATACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATG +AGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTATC +CCACCAGGGCAGATGAGAGAACCTAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAATAACATGGATGACA---------GGCAACC +CACCCGTC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA +CTCTAAGAGCTGAACAAGCTACACAGGAGGTAAAAAACTGGATGACAGAA +ACCTTGTTGGTC---CAAAATTCGAACCCAGATTGTAAGACAATTTTAAA +AGCATTGGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGCCATAAAGCAAGAATTCTGGCTGAGGCAATG--- +---------AGCAAAGCAACA------------------------AGTAC +AGCCATAATGATGCAGAAA---AGCAAC---TTTAAGGGC---CAAAAA- +--AGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAGA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGCACT---------GAA---AGGCAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAGG---------GGG--- +AGGCCAGGAAATTTTCTTCAGAAC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCGCCAGCA---GAGAACTTC +GGGTTCGGA---------------GAGGGGATA---ACCCCCTCC----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGGCGAG---------------------GAACAGGCT--- +---CCTCCC---TTA---GTTTCCCTCAAATCACTCTTTGGCAGCGACCC +TTAGTCGCAATAA +>Ref.F2.CM.95.95CM_MP257.AJ249237 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA +AAAAATTCGGTTAAGGCCGGGGGGGAAGAAAAAATATAGGCTGAAACATA +TAGTATGGGCAAGCAGGGAGCTAAAACGATTTGCACTTAATCCTGGCCTT +TTAGAGACAACAGAAGGCTGTAAGAAAATAATAGGACAACTACAACCATC +CCTTCAGACAGGGTCAGAGGAACTGAAATCATTATTTAACACAATAGTAG +TTCTCTATTATGTACATCAAAAGATAGAGGTAAGAGACACCAAGGAAGCT +TTAGATAAGCTACAGGAAGAACAA------------GAC----------- +----------AAA---------------CATCAG------CAAAAA---- +-----------------------------ACACAACAAGCAACGGCT--- +------------------------------GACAAAGGG----------- +-------------------------------------------------- +-----------------------------GTCAGTAAAGGG--------- +---------GTCAGTCAAAATTACCCTATACTACAAAATCTTCAGGGGCA +AATGGTACACCAGAGTCTATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGACCTATC +CCACCAGGTCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACCAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AGCAACC +CACCTGTC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA +CTCTAAGAGCTGAGCAAGCCACGCAGGAAGTAAAAGGCTGGATGACAGAA +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA +AGCATTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GTGTGGGAGGACCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATG--- +---------AGCAAAGCAACA------------------------GGTGC +AGCCATAATGATGCAGAAG---AGCAAC---TTTAAGGGC---CAAAGA- +--AGAATTGTTAAGTGTTTTAACTGTGGCAAAGAAGGACATATAGCTAGA +AATTGCAGGGCCCCTAGAAAAAGGGGCTGCTGGAAATGTGGACAGGAAGG +ACACCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATGTGG---CCT---TCCAACAAG---------GGG--- +AGGCCCGGAAATTTTCTTCAGAAC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCGCCAGCA---GAGAGCTTC +GGGTTCGGG---------------GAGGAGATA---GCTCCCTCC----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGACAAG---------------------GAACAGGTT--- +---CCTCCC---TTG---ATTTCCCTCAAATCACTCTTTGGCAGCGACCA +GTAGTCACAATAA +>Ref.F2.CM.97.CM53657.AF377956 +---------AGAGCGTCACTATTAAGCGGGGGAAAATTAGATGATTTGGA +AAAAATTCGGTTAAGGCCAGGGGGGAAGAAAAAATATAGGCTGAAACATA +TAGTATGGGCAAGCAGGGAGCTAGAAAGATTTGCACTTAATCCTGGCCTT +TTAGAGACAAAGGAAGGCTGTAAACAAATAATAGGACAACTACAACCATC +CCTTCAGACAGGATCAGAAGAGCTTAAATCATTATTCAACACAATAGTAG +TCCTCTATTATGTACATCAAAGGATAAAAATAGGAGACACCAAGGAAGCT +TTAGATAAGCTACAGGAAGAACAA------------GAC----------- +----------AAA---------------AGTCAG------CAAAAA---- +-----------------------------ACACAACCAGCAGCGGCT--- +------------------------------GACAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA +AATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCAGGCAGGACCCATC +CCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTAC +TAGCAACCTACAGGAACAAATAGCATGGATGACA---------AGCAACC +CACCTGTC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA +CTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAAGGCTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGATCATTTTAAA +AGGATTAGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GGGTGGGGGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATG--- +---------AGCCAAGTAACA------------------------TCTAC +ATCCATATTGATGCAGAAA---AGCAAC---TTTAAGGGC---CAAAGA- +--AGAAATGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAA +AATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCTGGAAATTTTCTTCAGAAC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCGCCAGCA---GAAAGCTTC +GGGTTCGGA---------------GAAGAGATA---ACTCCCTCC----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAAGACAAG---------------------GAAATGTAC--- +---CCTCCC---TTG---ACTTCCCTCAAATCACTCTTTGGCAACGACCC +TTAGTCACAATAA +>Ref.G.BE.96.DRCBL.AF084936 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA +GAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAGATATAGAATGAAACATT +TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTT +TTAGAAACAGCAGAAGGTTGTCAAAAAATAATGGCACAGTTGCAACCAGC +TCTCCAAACAGGAACAGAGGAGATTAAATCACTATTTAATACAGTAGCAA +CCCTCTATTGTGTACATCAAAAGATAGAGGTAAGAGACACCAAAGAGGCT +CTAGAGGAAGTGGAAAAGATACAA------------AAG----------- +----------AAG---------------AGTCAG------CAAAAA---- +-------------------------------------------------- +------------------------------GAA---AAC----------- +-------------------------------------------------- +-----------------------------AGCAGCAGCCAA--------- +---------GTCAGTCAAAATTACCCTATAGTGCAGAATGCACAAGGGCA +AATGGTACACCAGGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAG +TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTACA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAATAC +AGTGGGGGGGCATCAAGCAGCTATGCAAATGTTAAAGGAGACTATCAATG +ATGAAGCTGCAGAATGGGACAGGCTACATCCACAGCAGGCAGGGCCTATT +GCACCAGGCCAGATAAGGGACCCAACGGGAAGTGATATAGCAGGAGCTAC +TAGTACCCTGCAGGAACAGATAAGATGGATGACC---------AGCAACC +CACCTGTC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGG +TTAAATAAAATAGTAAGAATGTACAGCCCTGTCAGCATTTTGGACATAAG +ACAGGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGATTCTTTAAAA +CCCTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAAGCTGGATGACAGAC +ACCTTGTTGATC---CAAAATGCAAACCCAGATTGTAAGATCATCTTAAA +AGGATTAGGACAAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATG--- +---------AGCCAGGCATCAGGTGCA------------------GCAGC +AGCCATAATGATGCAGAAA---AGCAAT---TTCAAGGGC---CCAAGA- +--AGAACAATTAAATGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG +ACATCAAATGAAAGAATGCACA---------GAA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCAGGGAATTTCCTTCAGAAC-------------------------- +----AGGCCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCCGCA---GAGAACTTC +GGGTTCGGG---------------GAGGAGATA---GCCCCCTCC----- +-------------------CCGAAGCAGGAGCAG---------------- +--------AAGGAAAAG---------------------GAACTATAT--- +------CCT---CTA---TCTTCCCTCAAATCACTCTTTGGCAACGACCA +ATAGTCAAAGTAA +>Ref.G.KE.93.HH8793_12_1.AF061641 +ATGGGTGCGAGAGCSTCASTATTAAGCGGGGGAAAATTAGATGCATGGGA +AAAAATTCGSCTGACGCCAGGGGGAAAGAAAAAATACAGACTGAAACATC +TAGTATGGGCAAGCAGAGAGATGGAGAGATTTGCACTTAACCCTGGCCTT +TTAGAAACAGCAGAAGGTTGTCAACAAATAATGAGCCAGTTGCAACCAGC +TATCCAMACAGGAACAGAGGAGATTAAATCATTATTTAATACAGTAGCAA +CCCTCTATTGTGTACATCCCAAGATAGAGGTAAAGGACACCAAAGAAGCT +CTAGAGGAAGTAGAAAAGATACAA------------AAG----------- +----------AAA---------------AGTCAG------CAAAAA---- +-----------------------------ATACAGCAGGCAGCAAGG--- +------------------------------GATGAAGGA----------- +-------------------------------------------------- +-----------------------------AACAGCAGCCAA--------- +---------GTCAGCCAAAATTATCCTATAGTGCAGAACGCACAAGGACA +GATGGTACACCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG +TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACAC +AGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAAGATACTATCAATG +AGGAAGCTGCAGAGTGGGACAGAATACATCCACCACAGGCAGGGCCTATT +CCACCAGGCCAAATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACCAC +TAGTAACCTGCAGGAACAAATAAGATGGATGACC---------AGCAACC +CACCTATC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGACAGGTTCTTTAAAA +CTTTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACTATCTTAAG +AGCATTAGGACCCGGAGCTACACTAGAAGAAATGATGACAGCATGCCAGG +GAGTGGGAGGACCCGGCCATAAAGCAAGAGTGTTAGCTGAGGCAATG--- +---------AGCCAGGCAACAGGTGCA------------------GCAGC +AGCCATAATGATGCAGAAA---AGCAAC---TTTAAGGGC---CCGAAA- +--AGAAATATCAAGTGTTTCAATTGTGGCAAGGAAGGACACTTAGCCAGA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGCTGGAAATGTGGAAAGGAGGG +ACATCAAATGAAAGACTGCACG---------GAA---AGACAGGCTAATT +TTT-AGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCAGGGAATTTTCTTCAGAAC-------------------------- +----AGGCCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCCGCA---GAGAGCTTC +GGGTTCGGA---------------GAGGAAATA---GCCCCCTCC----- +-------------------CCGAAGCCAGAGCCG---------------- +--------AAGGAAAAG---------------------GAGATACAT--- +------CCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAGCGACCC +CTAGTCACAGTAA +>Ref.G.NG.92.92NG083.U88826 +GTGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATTCTTGGGA +AAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAGTATAAACTAAAACATA +TAGTATGGGCAAGCAGGGAACTGGGGAGATTTGCACTTAACCGTGACCTT +TTAGAAACAGCAGAAGGTTGTGTGCAAATAATGAAACAGTTGCAACCAGC +TCTCTAGACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAA +CCCTCTACTGTGTACATCAAAAGATAGAGGTAAAAGACACCAAAGAAGCT +CCAGAGGAAGTGGAAAAAATACAA------------AAG----------- +----------AAC---------------AGTCAG------CAAGAA---- +-----------------------------ATACAGCAGGCAGCAAAG--- +------------------------------AATGAAGGA----------- +-------------------------------------------------- +-----------------------------AACAGTAACCCA--------- +---------GTCAGCCAAAATTATCCTATAGTGCAGAATGCACAAGGGCA +AATGATACATCAGGCCATATCACCTAGGACTTTGAATGCGTGGGTAAAAG +TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAGGGAGCCACCCCACAAGATTTAAATACCATGCTAAATAC +AGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATCAATG +ATGAAGCTGCAGAGTGGGACAGGATACATCCACAGCAGGCAGGGCCTATT +CCACCAGGCCAAATAAGAGAGCCTAGTGGAAGTGATATAGCAGGAACTAC +TAGTACCCTGCAGGAACAAATAAGATGGATGACC---------AGCAACC +CACCTATC---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAA +CTTTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGTTGGATGACAGAC +ACCTTGTTGGTT---CAAAATGCGAACCCAGATTGTAAAACCATCTTAAG +AGCATTAGGACCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATG--- +---------AGCCAGGCATCAGGTGCA------------GCA---GCAGC +AGCCATAATGATGCAGAAA---AGCAAT---TTTAAGGGC---CCGAGA- +--AGAATTATTAAGTGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG +ACATCAAATGAAAGAATGCACG---------GAA---AGGCAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCAGGAAACTTTCTCCAGAAC-------------------------- +----AGGACA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGATTCGGA---------------GAGGAGATA---GCCCCCTCC----- +-------------------CCGAAGCAGGAGCCA---------------- +--------AAGGAGAAG---------------------GAGCTATAT--- +------CCC---TTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC +CTAGTCACAGTAA +>Ref.G.PT.x.PT2695.AY612637 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA +AAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATT +TAGTATGGGCAAGCAGGGAGCTGGAAAAATTTGCACTCAACCCTGACCTT +TTAGAAACAGCAGAAGGTTGTCAACAAATAATGAGACAGTTACAACCAGC +TCTCCAGACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAA +CACTCTATTGTGTACATCAAAGGATAGAGGTAAAAGACACCAAAGAAGCT +CTAGAGGAAGTGGAAAAGACACAG------------AAG----------- +----------AAA---------------AGTCAG------AAACAA---- +--------------------------------CAGCAGGCAGCAATG--- +------------------------------GACGAAGGA----------- +-------------------------------------------------- +-----------------------------AACAGCAGCCAA--------- +---------GTCAGCCAAAATTATCCTATAGTGCAGAATGCACAAGGGCA +AATGGTACATCAGGCCATATCACCCAGAACTTTAAATGCATGGGTAAAAG +TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACAC +AGTAGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATTAATG +AGGAAGCTGCAGAGTGGGACAGGATACATCCACAACAGGCAGGGCCTATC +CCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTGCAGGAACAAATAAGATGGATGACC---------AGCAATC +CACCTATC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGATATAAG +ACAAGGGCCAAAAGAACCTTTTAGAGATTATGTAGATAGGTTCTTTAAAA +CTTTAAGAGCTGAACAAGCTACACAGGAAGTAAAAGGCTGGATGACAGAC +ACCTTGCTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATCTTAAG +AGCATTAGGACCAGGAGCTTCACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCCAGTCACAAAGCAAGAGTTTTAGCTGAGGCAATG--- +---------AGCCAGGCATCA------------------------GGGGC +AACAATAATGATGCAAAAA---AGCAAC---TTTAAGGGT---CCAAAA- +--AGAATGATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG +ACACCAAATGAAAGACTGCACA---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- +AGGCCAGGGAATTTTCTCCAGAAC-------------------------- +----AGGCCC------GAGCCAACAGCC---------------------- +-----------------------------CCACCCGCA---GAGAGCTTC +GGGTTCGGA---------------GAGGAGATA---GCCCCCTCC----- +-------------------CCGAAGCAAGAGCCG---------------- +--------AAGGACAAG---------------------GAGTTATAC--- +------CCC---TTA---ACCTCCCTCAAATCACTCTTTGGCAGCGACCC +CTAGTCACAGTAA +>Ref.H.BE.93.VI991.AF190127 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGGCTAAAACATC +TGGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGACCTT +TTAGAAACAGCAGATGGCTGCCAACAAATACTAGGACAGCTACAGCCAGC +TCTTAAGACAGGAACAGAAGACCTTCAATCATTATATAATACAATAGCAG +TCCTCTATTGCGTACATCAAAGAATAGATGTGAAAGACACCAAGGAAGCT +TTAGGGAAGATAGAGGAAATACAG------------AAT----------- +----------AAG---------------AACAAG------CAAAGA---- +-----------------------------ACACAGCAGGCCCCAGCA--- +------------------------GCAGCTGATAAAGAA----------- +-------------------------------------------------- +-----------------------------AAGGACAGCAAG--------- +---------ATCAGTCAAAATTATCCTATAGTACAGAATGCCCAGGGGCA +AATGGTACACCAGGCAATATCACCTAGGACCTTAAATGCATGGGTAAAAG +TAGTAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCCATGCTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATG +AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTACATGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTTCAGGAACAAGTAGCATGGATGACA---------GGCAATC +CCCCAATT---CCAGTGGGAGACATCTATAAGAGATGGATAATCCTGGGA +TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA +ACAAGGACCAAAAGAACCCTTCAGAGACTATGTAGACAGGTTCTTTAGAG +TTTTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAACTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGCAGGACTATTTTAAA +AGCATTAGGACGAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCAAGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGTAACAAATGCA------------------AGTGC +AGCCATAATGATGCAGAAA---GGCAAC---TTTAAGGGC---CCAAGA- +--AGAACTGTTAAATGTTCCAACTGTGGCAAAGAAGGACACATAGCCAGA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGACAGGAAGG +ACACCAGATGAAAGACTGCACA---------GGA---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAGCAAG---------GGA--- +AGGCCAGGGAATTTCCCCCAGAAG-------------------------- +----AGGCTA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCGGA---------------GAGGAGATC---ACCCCCTCT----- +-------------------CCGAGGCAGGAGCTG---------------- +--------AAAGAACAG---------------------GAACCT------ +------CCT---TTA---ACTTCCCTCAGATCACTCTTTGGCAACGACCA +ATAGTCACAGTAA +>Ref.H.BE.93.VI997.AF190128 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACGATTAGATACTTTGGA +GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATA +TAGTATGGGCAAGCAGAGAGCTGGAAAGATTTGCACTTAACCCCGGCCTT +TTAGAATCAGCAGAAGGCTGTCTACAAATAATAGAACAACTACGGCCATC +TATTAAGACAGGAACAGAAGAACTTCWATCATTATTTAATACCGTAGCGA +CCCTCTATTGCGTACTTCAAAGAATAGAGGTAAAAGACACCAAGGAAGCT +TTAGGGAAGATAGAGGAAATACAA------------AAC----------- +----------AAA---------------AGGCAG------CAAAAA---- +-----------------------------ACACAGCAAGCAACAGCT--- +------------------------------AATAAGGAA----------- +-------------------------------------------------- +-----------------------------AGAGACAACAAG--------- +---------GTCAGTCAAAATTATCCTATAGTACAGAATGCTCAAGGGCA +GATGGTACACCAGCCCATATCACVTAGGACCTTAAATGCATGGGTAAAAG +TAGTAGAG---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATG +AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCTGGAACTAC +TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------GGCAATC +CAAGTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAGATAGTAAGAATGTATAGTCCTGTTAGTATTCTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA +CTTTAAGAGCTGAGCAAGCCACACAGGAGGTGAAGAATTGGATGACAGAC +ACCTTGTTGGTC---CAGAATGCAAATCCAGATTGCAAGACTATTTTAAG +AGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGTAACAAATGCA------------------AATGC +AGCCATAATGATGCAGAAA---AGCAAC---TTTAAGGGC---CCAAGA- +--AAAATTGTTAAATGTTTCAATTGTGGCAAAGAGGGACACATAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAGGGAAGG +ACATCAGATGAAGGACTGCACA---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATCTGG---CCT---TCCAGCAAA---------GGG--- +AGGCCAGGAAATTTTCTCCAGAGC-------------------------- +----AGGCCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCGGG---------------GAGGAGATG---ACCTCCTCC----- +-------------------CCGAAGCAGGAGCTG---------------- +--------AAGGACAAG---------------------GAACCT------ +------CCC---TTT---GCTTCCCTCAAATCACTCTTTGGCAACGACCC +CTTGTCACAGTAA +>Ref.H.CF.90.056.AF005496 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATGCTTGGGA +GAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATC +TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGGCCTT +TTAGAAACACCAGAAGGCTGTCTACAGATAATAGAACAGATACAGCCAGC +TATTAAGACAGGAACAGAAGAACTTAAATCATTATTTAATCTAGTAGCAG +TCCTCTATTGCGTACATCGAAAAATAGATGTGAAAGACACCAAGGAGGCT +TTAGATAAGATAGAGGAAATACAA------------AAC----------- +----------AAA---------------AGTCAG------CAAAAA---- +-----------------------------ACACAGCAAGCAGCAGCT--- +------------------------------GATAAGGAA----------- +-------------------------------------------------- +-----------------------------AAAGACAACAAG--------- +---------GTCAGTCAAAATTATCCTATAGTACAGAATGCTCAAGGGCA +GATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAG +TAGTAGAA---GAAAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATAC +AGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACAATCAATG +AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTGCATGCAGGGCCTATT +CCACCAGGCCAAATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTAC +TAGTACCCTGCAGGAACAAATAGCATGGATGACA---------GGCAATC +CAGCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA +TTAAATAAGATAGTAAGAATGTATAGTCCTGTCAGCATTCTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTTTTTAAAA +CTTTAAGAGCTGAGCAAGCCACACAGGATGTGAAGAATTGGATGACAGAA +ACCTTGTTGGTC---CAAAATGCAAATCCAGATTGCAAGACTATATTAAG +AGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGCCAAGTAACAAATACA------------------AATAC +AGCCATAATGATGCAGAAA---GGCAAC---TTTAAGGGC---CAAAGA- +--AAATTTGTTAAATGCTTCAACTGTGGCAAAGAGGGACACATAGCCAGA +AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAGAGAAGG +ACATCAGATGAAAGACTGCACA---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATTTGG---CCT---TCCAGCAAA---------GGG--- +AGGCCAGGAAATTTTCTCCAGAGC-------------------------- +----AGGCCA------GAACCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCGGA---------------GAGGAGATG---ACCCCCTCT----- +-------------------CCGAAGCAGGAGCAG---------------- +-----CTGAAGGACAAG---------------------GAACCT------ +------CCC---TTA---GCTTCCCTCAGATCACTCTTTGGCAGCGACCC +CTTGTTACAGTAA +>Ref.H.GB.00.00GBAC4001.FJ711703 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA +GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATC +TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTCAACCCCGACCTT +TTAGAAACAGCAGATGGCTGTCTAAAAATAYTAGGACAGATACAGCCAGC +TCTTCAGACAGGAACAGAAGAAATTAAATCGTTATTTAATCTAGTAGCAG +TCCTCTATTGTGTACATCAGAAAATAGAGGTACAAGATACCAGTGAAGCT +TTAAATAAGGTAAAGGAGATACAG------------AAC----------- +----------AAG---------------AACCAG------CAAACA---- +-----------------------------ACACAGCAGGCAACAGCT--- +------------------------------RGTAAAGAG----------- +-------------------------------------------------- +-----------------------------AAGGACAGCAAG--------- +---------ATCAGTCAAAATTATCCTATAGTACAGAATGCCCAAGGGCA +AATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAG +TAGTAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGARGGAGCMACCCCACAAGACYTAAATACCATGTTAAACTC +AGTGGGGGGACATCAGGCAGCCATGCAAATRTTAAAAGATACAATCAATG +AGGAAGCTGCAGAATGGGATAGGACACATCCAGTGCATGCAGGGCCTATT +CCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTAC +TAGYAACCTTCAGGAACAAATAGCATGGATGACA---------RGYAATC +CCCCTRTC---CCAGTGGGRGAKATCTATAAAAGATGGATAATCWTGGGA +TTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAA +ACAAGGGCCAAAAGAACCCTTTAGAGAYTATGTAGACAGGTTYTTTAAAA +CTTTAAGAGCTGAGCAAGCCACACAGGACGTGAAGAATTGGATGACAGAC +ACCTTGTTGGTC---CAAAATGCAAATCCAGATTGCAAGACTATTTTAAA +AGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- +---------AGTCAAATGACAAATATG------------------AATAC +AGCCATAATGGTGCAGAAA---GGCAAC---TTTAAGGGC---CAAAGA- +--AGAACTGTTAAATGTTTCAACTGTGGTAAAGAAGGACACATAGCAAGA +AACTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGAGGGAAGG +ACATCAGATGAAAGACTGCACA---------GAG---AGACAGGCGAATT +TTTTAGGGAAAATCTGG---CCT---TCCAGCAAA---------GGG--- +AGGCCAGGGAACTTTCTCCAGAGC-------------------------- +----AGGCCA------GAACCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAATGCTTC +GGGTTCGGG---------------GAGGAGATG---ACACCCCCT----- +-------------------CCGAAGCAGGAGATG---------------- +--------AAGGAAAAG---------------------GAACCT------ +------CCC---TTA---ACTTCCCTCAGATCACTCTTTGGCAGCGACCC +CTTGTCACAGTAA +>Ref.J.CD.97.J_97DC_KTB147.EF614151 +------------------------------------------GCATGGGA +GAAAATTTGGCTGAGGCGACGGGGAGAGAAAAAATACAGGCGAAAACATA +TAGTATGGGCAAGCAGGGAGCTGGACAGATATGCACTTAACCCTGGCCTT +CTATAGTGAGCAGAAGGCGGTGAACAGATACTAGTACAGATCCAACCAGA +TCTTTAAACAGGAGCAGAGGAGATAAAATCATTATTTAACACAGAAGCAA +CCCTCTATTGTGTACATTAGAGGATAGACATAAGAGACACCAAGGAGGCT +TTAGACAAGATAGAGGAACTTTAA------------AAC----------- +----------AAA---------------AGCAAG------GAGAAA---- +-----------------------------GCTAAGAAAGAA---GCT--- +------------------------------GTCAAAAAA----------- +-------------------------------------------------- +-----------------------------TACAACAGTCAG--------- +---------GTGAGTCACAATTATCCTATATTGCAAAATATGTAAGGGGA +ACTAGTACACCAGGCCCTATCACCTAGAACATTAAATGCATGGGTAAAGG +TGATAGAA---GAGAAAGGTTTCAACCCAGAAGTGATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACTCCACAAGATTTAAATACCATGCTAAACAC +GGTGGGGGGACATCAAGCAGCGATGCAAATGTTAAAAGATACCATCAATG +AGGAAGCTGCAGAATGGGACAGGCTCCATCCAGTACATGCAGGACCTGTT +GCACCAGGTCAGATGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTAC +TAGTAACCTTCAGGAACAAATAGCATGGATAACAGGCAACGGTGGCAACC +AACCTATC---CCAGTAGGAGAAATCTATAAAAGATGGATAATTTTAGGA +TTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +GCAAGGACCAAAAGAACCTTTTAGAGACTATGTGGATAGGTTCTTTAAAA +CTCTAAGAGCCGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGAT +ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGTAAGACCATTCTAAG +AGCATTAGGAGCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGAGAGTATCCAGTCATAGAGCAAGAGTTTTTGGTGAGGCAATA--- +---------AGCCAAGTAAAC------------------------AATAC +AAACATAATAATGCAAAGA---GGTAAC---TTTAGGGGC---CAGAAG- +--AGAAGTGTTAAATGTTTCAACTGTGGTAAAGAGGGACACATAGCAAAA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGAAAGTGTGGAAAGGAAGG +ACACCAAATAAAAAACTGCACT---------GAG---AGACAGGCCAATT +TTTTAGGGAAAGTTTGG---CCT---TCCAGCAAG---------GGG--- +AGGCCAGGGAACTTTCTCCAGAGC-------------------------- +----AGGCCA------GAACCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAAAGCTTC +GGGTTCGGG---------------GAGAAGATA---ACTCCCTCC----- +-------------------CAGAAACAGGAACCG---------------- +--------AGGAAG------------------------GAACTATAT--- +------CCT---TCA---GCTTCCCTCAAATCACTCTTTGGCAGCGACCC +CTCGTCACAGTAA +>Ref.J.CM.04.04CMU11421.GU237072 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATACTTGGGA +GAAAATTCGGTTGAGGCCAGGGGGGAAGAAACGTTATAGGCTAAAACATT +TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGRCCTT +CTAGAAACATCAAAAGGCTGTCAACAAATATTAGTACAGCTCCAACCATC +TTATCAAACAGGGACAGAAGAAATTAAGTCATTATATAACACAGTAGCAA +CCCTCTATTGCGTACATGAGGRSATAGAGGTAAAAGACACCAAGGAARCT +TTAGACAAGATAGAGGAACTACAA------------AAG----------- +----------AAG---------------AACAAG------CAACAG---- +-----------------------------GCACAGAAAGCAGAARCT--- +------------------------------GACAAAAGR----------- +-------------------------------------------------- +-----------------------------RACARCAGTCAA--------- +---------GTCAGTCAAAATTATCCTATAGTGCAGAACATGCAAGGGCA +ACCAGTACAYCARGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAG +TGRTAGAA---GARAAGGCTTTYAGCCCAGAAGTAATACCCATGTTTTCA +GCYTTATCAGAAGGAGCCACCCCRCAAGATTTAAATACCATGCTAAATAC +AGTRGGGGGACACCARGCAGCTATGCAAATGTTAAAAGATACTATCAATG +AGGAAGCTGCAGAATGGGATAGGKTACATCCAGTACATGCAGGGCCTCCR +GCACCAGGCCAGGCGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTCCAGGAACAAATAGCATGGATGACA---------GGCAACC +CACCTATC---CCAGTAGGGGAAATTTATAAAAGRTGGATAATTCTGGGA +TTAAATAAAATAGTRAGAATGTATAGCCCTGTCAGCATTTTGGATATAAG +ACAAGGACCAAAAGARCCTTTTAGAGAYTATGTAGATCGGTTCTTTAAAA +CTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGAT +ACCTTGTTGATC---CAAAATGCAAATCCAGATTGCAGAACCATYTTAAA +AGCATTAGGACCAGGAGCTACACTAGARGAAATGATGACAGCATGYCAGG +GAGTGGGAGGACCTGGTCATAAAGCAAGAGTTTTGGCWGAAGCAATG--- +---------AGCCAAATGACCAAT---------------------ACAGC +AAACATAATGATGCAAARG---GGTAAY---TTTAAGGGC---CARAAA- +--AGAATGATTAAGTGTTTCAATTGTGGWAAACCAGGACACCTAGCMAGA +AAYTGCAGAGCCCCTAGRAARAAGGGCTGTTGGAAATGTGGACAGGAAGG +ACAYCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAARATCTGG---CCT---TCCAACAAR---------GGG--- +AGGCCAGGGAACTTTCTYCAGAGC-------------------------- +----AGRCCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCGGG---------------GAAGAGACC------YCYYCC----- +-------------------CCGAAACAAGAAGCG---------------- +--------AAG---------------------------GAACTGTAT--- +------CCT---CTA---ACTTCCCTCAAATCACTCTTTGGCARCGACCC +CTYGTCACAATAA +>Ref.J.SE.93.SE9280_7887.AF082394 +ATGGGTGCGAGAGCGTCAATATTAAGTGGGGGAAAATTAGATGATTGGGA +AAAAATTCGGTTGAGGCCAGGGGGGAAGAAAAAATATAGGATAAAGCATC +TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTT +CTAGAGTCAGCAAAAGGCTGTCAACAAATACTAGTACAGCTCCAACCAGC +TCTCCAGACAGGAACACAAGAAATTAAATCATTGTATAATACAGTAGCAA +CCCTCTATTGCGTACATCAGAGGATAGAAATAAAAGACACCATGGAAGCT +TTAGAGAAGATAGAGGAAATTCAA------------AAC----------- +----------AAG---------------AACAAA------CAGCAG---- +-----------------------------GCACAGAAAGCAGAAACT--- +------------------------------GACAAAAAA----------- +-------------------------------------------------- +-----------------------------GACAACAGTCAG--------- +---------GTCAGTCAAAATTATCCTATAGTGCAGAATCTGCAAGGGCA +ACCGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAG +TGATAGAA---GAAAAAGCTTTCAGCCCAGAAGTGATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACAC +AATAGGGGGACACCAAGCAGCTATGCAAATGTTAAAAGATACTATCAATG +AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATT +GCACCAGGCCAGGTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC +TAGTACCCTCCAGGAACAAATAGGATGGATGACA---------GGCAATC +CACCTATC---CCAGTAGGAGAGATTTATAAAAGATGGATAATTCTGGGA +CTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAG +ACAAGGACCAAAAGAACCTTTTAGAGACTATGTAGACAGGTTCTTTAAAG +CTCTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAATTGGATGACAGAT +ACCTTGCTGGTC---CAAAATGCAAATCCAGATTGCAAGACCATTTTAAA +AGCATTAGGATCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG +GAGTGGGAGGACCTGGTCATAAGGCGAGAGTTTTGGCTGAAGCAATG--- +---------AGCCAAGTGACC------------------------AATAC +CAACATAATGATGCAAAGA---GGTAAC---TTTAGGGAC---CATAAA- +--AGAATTGTTAAGTGTTTCAATTGTGGCAAACAAGGACACATAGCAAAA +AACTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG +ACACCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAGATTTGG---CCT---TCCAGCAAA---------GGG--- +AGGCCAGGGAACTTTCTCCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCCTC +GGGCTCGGA---------------GAGGAGATC------CCCTCC----- +-------------------CCGAAACAGGAGCCG---------------- +--------AAGGACAAG---------------------GAACTGTAT--- +------CCT---CTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC +CTTGTCACAATAA +>Ref.K.CD.97.97ZR_EQTB11.AJ249235 +ATGGGTGCGAGAGCTTCAGTATTAAGCGGGGGAAAATTAGACAAATGGGA +AAAAATTCAGTTACGGCCAGGGGGAAAGAAAAAATACAGGCTAAAACATC +TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTAACCTT +TTAGAGACAGTAGAAGGCTGTCGGCAAATAATAAGACAACTACAACCATC +CCTTCAAACAGGCTCGGAAGAGCTTAGATCACTATTTAATACAGTAGCAA +CCCTCTATTGGGTGCATCAAAGTATACAGGTAAGGGACACCAAGGAAGCC +TTAGACAAACTAGAGGAAGAACAA------------AAC----------- +----------AGA---------------ACTCAG------CAAAAG---- +-----------------------------ACACAGCAAGGAAAAGCT--- +------------------------------GACAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTTAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGGCA +AATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTTAAAG +TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA +GCATTATCAGAAGGAGCCACTCCACAAGATTTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATG +AGGAAGCTGCAGAATGGGACAGGATGCACCCAGTGCAAGCAGGGCCTATC +CCACCAGGCCAAATAAGAGAACCTAGGGGGAGTGATATAGCAGGAACTAC +TAGCACTCTTCAGGAACAAATAACATGGATGACA---------AGCAACC +CACCTATC---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGG +TTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAGAG +TTCTAAGAGCTGAACAAGCCACACAGGAAGTAAAAAATTGGATGACAGAA +ACCCTGTTGGTC---CAAAACGCAAACCCAGATTGTAGGACCATTTTAAA +GGCGTTGGGATCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGG +GAGTAGGAGGGCCTGGCCATAAAGCAAGGGTTTTGGCTGAGGCAATG--- +---------AGCCAGGTAACA------------------------AATTC +AGCCGTAATGATGCAGAGA---GGCAAC---TTTAAGGGT---CAAAGA- +--AGAATTATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGA +AATTGTAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGGAAAGAAGG +ACATCAGATGAAAGACTGTTCT---------GAG---AGACAGGCTAATT +TTTTAGGGAAGTTCTGG---CCT---CTCAACAAA---------GAG--- +AGGCCAGGAAATTTTCTTCAGAAC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTT +GGGTTCGGG---------------GAGAAGATA---ACCCCCTCT----- +-------------------CTGAGACAGGAAATG---------------- +--------AAAGATCAG---------------------GAACAGGGT--- +---CCTCCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC +GTTGTCACAGTAA +>Ref.K.CM.96.96CM_MP535.AJ249239 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA +AAAGATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAAACTGAAACATC +TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTCAACCCTGGCCTT +TTAGAGACAACAGAAGGCTGTCGGCAAATAATAACACAAATACAGCCATC +CATTCAAACAGGATCAGAAGAGATTAAATCACTATATAATACAATAGCAG +TCCTCTATTTTGTACATCAAAAGATAGAGGTAAAAGACACCAAGGAAGCC +TTAGACAAACTAGAGGAAGAACAA------------AAC----------- +----------AAA---------------AGTCAG------CGAAAG---- +-----------------------------ACACAACAAGAAGCAGCT--- +------------------------------GACAAAGGG----------- +-------------------------------------------------- +-------------------------------------------------- +---------GTCAGTCAAAATTACCCTATAGTACAGAATCTGCAGGGGCA +AATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTGAAGG +TAATAGAG---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTACA +GCATTATCAGAAGGAGCCACTCCACAAGATCTAAACACCATGCTAAACAC +AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATG +ATGAAGCTGCAGAATGGGACAGGTTACACCCAGTGCATGCAGGGCCTATC +CCACCAGGCCAAATGAGAGAACCGAGGGGGAGTGACATAGCAGGAACTAC +CAGCACCCTTCAGGAACAAATAGCATGGATGACA---------AGCAACC +CACCTGTC---CCAGTGGGGGAAATCTATAAAAGATGGATAATCCTGGGT +TTAAACAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG +ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAA +CCCTAAGAGCTGAACAAGCCACACAGGAAGTAAAGAATTGGATGACAGAC +ACCCTGTTGGTC---CAAAACGCAAACCCAGATTGTAAGACCATTTTAAA +AGCGTTGGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGG +GAGTGGGAGGGCCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATG--- +---------AGCCAGGTAACA------------------------AATCC +AGTTGTAATGATGCAGAAA---GGCAAC---TTTAAGGGC---CATAGA- +--AAAATTGTTAAGTGCTTCAACTGTGGCAAAGAAGGGCACATAGCCAGA +AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGGAAGGAAGG +ACATCAGATGAAAGACTGCACT---------GAG---AGACAGGCTAATT +TTTTAGGGAAAATCTGG---CCT---TCCCACAAG---------GGG--- +AGGCCAGGGAATTTTCTTCAGAGC-------------------------- +----AGACCA------GAGCCAACAGCC---------------------- +-----------------------------CCACCAGCA---GAGAGCTTC +GGGTTCGGG---------------GAGGAGATA---ACCCCCTCT----- +-------------------CCGAGGCAGGAGACC---------------- +--------AAAGACAAG---------------------GAACAGAGC--- +---CCTCCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCC +ATTGTCACAATAA diff -Nru bppsuite-0.6.2/Examples/Data/HIV1_REF_2010_gag_macse_AA.fasta bppsuite-0.7.0/Examples/Data/HIV1_REF_2010_gag_macse_AA.fasta --- bppsuite-0.6.2/Examples/Data/HIV1_REF_2010_gag_macse_AA.fasta 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/Data/HIV1_REF_2010_gag_macse_AA.fasta 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,78 @@ +>Ref.D.CD.83.ELI.K03454 +MGARASVLSGGKLDKWEKIRLRPGGKKKYRLKHIVWASRELERYALNPGLLET-SEGCKQIIGQLQP-AIQTGTEELRSLYNTVATLYCVH-KGIDVKDTKEALEKMEEE-QNKSK---KKAQQA--AADTGNNS------QVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIAWMTSN---PPIPVGEIYKRWIIVGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNANPDCKTILKALGPQATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---NSVTT---AMMQRGNFKGPRKIIKCFNCGKEGHIAKNCRAPRKKGCWR-CGKEGHQLKDCTERQANFLGRIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEIT-PSQKQEQ-KD--KEL---YPLTSLKSLFGNDPLSQ*- +>Ref.C.ET.86.ETH2220.U46016 +MGARASILRGEKLDAWEKIKLRPGGKKHYMLKHLVWANRELEKFALNPDLLDT-SAGCKQIIKQLQP-ALQTGTEELKSLFNTVATLYCVH-QKIEIKDTKEALDKIEEE-QNESQ---QKTQQA-GAADRG---------KDSQNYPIVQNMQ-GQMVHQPISARTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMRDPRGSDIAGTTSTLQEQIAWMTGN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPAHKARVLAEAMS--QV--N---N--TT---IMMQKSNFKGPKRAIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGRLWPSNKGRPGNFLQSRP----------EPTAPPESLRPEPTAPPPESFRF-EEAT-PSPKQEL-KD--RE-----ALTSLKSLFGNDHLLQ*- +>Ref.C.ZA.04.04ZASK146.AY772699 +MGARASVLRGEKLDTWEKIRLRPGGKKHYMLKHIVWASRELERFALNPGLLET-SEGCKQILAQIQP-AIQTGTEELKSLFNTIAVLYCVH-KKIDVRDTKEALDKIEEE-QNKSQ---QKTQQA-KAADE----------KVSQNFPIVQNLQ-GQMVHQPLSPRTLNAWVKVIEEKGFNPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQVAWMTSN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMAACQGVGGPGHKARVLAEAMS--QI--N---N--GN---IMMQRSNFKGPKRIVKCFNCGKGRHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSQKGRPGNFLQNRL----------EPTAPPA-----------ESFRF-EETT-PAPKQEL-KD--RE-----PLTSLRSLFGSDPLSQ*- +>Ref.A1.UG.92.92UG037.AB253429 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALNPSLLET-TEGCQQIMEQLQS-ALRTGTEELRSLYNTVATLYCVH-QRIEVKDTKEALDKIEEI-QKKSK---QKTQQA--AADTGSSS------KVSQNYPIVQNAQ-GQMIHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTPQEQIAWMTGN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLIQNANPDCKSILRALGAGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--Q---H--TN---IMMQRGNFKGQKR-IKCFNCGKEGHLAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFPQSRP----------EPTAPPAA----------EIFGMREEIV-SPPKQEQ-ND--RDQ--NPPSVSLKSLFGNDLLSQ*- +>Ref.A1.RW.92.92RW008.AB253421 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRMKHLVWASRELERFALNPGLLET-TEGCQKIIEQLQP-SVKTGTEELKSLFNTVATLYCVH-QRIDVKDTKEALDKIEEM-QNKSK---QKTQQA--AADIGNSS------KVSQNYPIVQNAQ-GQMIYQSMSPRTLNAWVKVIEEKGFNPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAADWDRLHPVQAGPIPPGQMREPRGSDIAGTTSTPQEQIGWMTSN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDVKQGPKEPFRDYVDRFFKILRAEQATQDVKHWMTETLLIQNANPDCKSILRALGTGATLEEMMTACQGVGGPSHKARVLAEAMS--QV--Q---H--PN---IMMQRGNFRGQKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSSKGRPGNFPQSRP----------EPSAPPA-----------EIFGIGEEIA-SPPKQEQ-KD--REP--AQPLVSLKSLFGNDPLSQ*- +>Ref.H.BE.93.VI997.AF190128 +MGARASVLSGGRLDTLEKIRLRPGGKKKYRLKHIVWASRELERFALNPGLLES-AEGCLQIIEQLRP-SIKTGTEEL?SLFNTVATLYCVL-QRIEVKDTKEALGKIEEI-QNKRQ---QKTQQA--TANKERDN------KVSQNYPIVQNAQ-GQMVHQPIS?RTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNAMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTGN---PSIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILRALGQGASIEEMMTACQGVGGPSHKARVLAEAMS--QV--T---N--ANA-AIMMQKSNFKGPRKIVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEMT-SSPKQEL-KD--KE----PPFASLKSLFGNDPLSQ*- +>Ref.H.BE.93.VI991.AF190127 +MGARASVLSGGKLDAWEKIRLRPGGRKKYRLKHLVWASRELERFALNPDLLET-ADGCQQILGQLQP-ALKTGTEDLQSLYNTIAVLYCVH-QRIDVKDTKEALGKIEEI-QNKNK---QRTQQAPAAADKEKDS------KISQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNAMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQVAWMTGN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFRVLRAEQATQDVKNWMTDTLLVQNANPDCRTILKALGRGASIEEMMTACQGVGGPSHKARVLAEAMS--QV--T---N--ASA-AIMMQKGNFKGPRRTVKCSNCGKEGHIARNCRAPRKKGCWK-CGQEGHQMKDCTGRQANFLGKIWPSSKGRPGNFPQKRL----------EPTAPPA-----------ESFGFGEEIT-PSPRQEL-KE--QE----PPLTSLRSLFGN!PIVTV! +>Ref.G.PT.x.PT2695.AY612637 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRMKHLVWASRELEKFALNPDLLET-AEGCQQIMRQLQP-ALQTGTEELRSLFNTVATLYCVH-QRIEVKDTKEALEEVEKT-QKKS----QKQQQA--AMDEGNSS------QVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRIHPQQAGPIPPGQIREPRGSDIAGTTSTLQEQIRWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMS--QA--S---G--AT---IMMQKSNFKGPKRMIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIA-PSPKQEP-KD--KEL---YPLTSLKSLFGSDP!VTV! +>Ref.K.CM.96.96CM_MP535.AJ249239 +MGARASVLSGGKLDAWEKIRLRPGGKKKYKLKHLVWASRELERFALNPGLLET-TEGCRQIITQIQP-SIQTGSEEIKSLYNTIAVLYFVH-QKIEVKDTKEALDKLEEE-QNKSQ---RKTQQE--AADKG----------VSQNYPIVQNLQ-GQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINDEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILKALGPGASLEEMMTACQGVGGPSHKARILAEAMS--QV--T---N--PV---VMMQKGNFKGHRKIVKCFNCGKEGHIARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEIT-PSPRQET-KD--KEQ--SPPLTSLKSLFGNDPLSQ*- +>Ref.F2.CM.97.CM53657.AF377956 +---RASLLSGGKLDDLEKIRLRPGGKKKYRLKHIVWASRELERFALNPGLLETK-EGCKQIIGQLQP-SLQTGSEELKSLFNTIVVLYYVH-QRIKIGDTKEALDKLQEE-QDKSQ---QKTQPA--AADKG----------VSQNYPIVQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVQAGPIPPGQIREPRGSDIAGTTSNLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQASQEVKGWMTDTLLVQNANPDCKIILKGLGTGATLEEMMTACQGVGGPGHKARILAEAMS--QV--T---S--TS---ILMQKSNFKGQRRNVKCFNCGKEGHIAKNCRAPRKRGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIT-PSPKQEQ-KD--KEM--YPPLTSLKSLFGNDP!VTI! +>Ref.F1.FI.93.FIN9363.AF075703 +MGARASVLSGGKLDAWEKIRLRPGGKKQYRIKHLVWASRELERFAIDPGLLET-SEGCQKIIAQIQP-SIQTGSEELRSLYNTIAVLYFVH-QKIEVKDTKEALDKLEEE-QNKSQ---QKTQQAAAAADKG----------VSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIQWMTSN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKALRAEQATQEVKGWMTDTLLVQNANPDCKIILKGLGIGATLEEMMTACRGVGGPGHKARILAEAMS--QA------N--TT---IMMQKSNFRGQRRIVKCFNCGKEGHIARNCRAPRKKGCWK-CGQEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQSRP----------EPTAPPA-----------ESLGIREEVT-PSPRQEQ-KE--EGQ--YPPLASLKSLFGNDP!VTI! +>Ref.D.UG.94.94UG114.U88824 +MGARASVLSGGKLDEWEKIRLRPGGKKKYRLKHLVWASRELERFALNPGLLET-SEGCRQIIRQLQP-SIQTGSEEIKSLYNTVVTLYCVH-ERIKVASTKEALDKIEEE-QAKSK---KKAQQA--TADTRNSS------QVSQNYPIVQNLQ-GQMVHHPLSPRTLNAWVKVIEEKAFNPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQLREPRGSDIAGTTSNLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---N--ANT-AIMMQRGNFKGPKKIIKCFNCGKEGHTAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSHNGRPGNFLQSRP----PA----EPTAPPA-----------EIFGLGEEIT-PPQKQEQ-KD--KEL---YPLTSLKSLFGNDPLSQ*- +>Ref.F1.BR.93.93BR020_1.AF005494 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALDPGLLET-SEGCRKIIGQLQP-SLQTGSEELKSLYNTIAVLYYVH-QKVEVKDTKEALEKLEEE-QNKGR---QKTQQA--TAEKG----------VSQNYPIVQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPTQAGPIPPGQIREPRGSDIAGTTSTLQEQIQWMTGN---PPVPVGEMYKRWIILGLNKIVRMYSPVGILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---N--TA---IMMQKSNFKGQRRIVKCFNCGKEGHIAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSNKGRPGNFIQNRP----------EPSAPPA-----------ESFRFGEETT-PSPKQEQ-KD--EGL--YPPLASLKSLFGNDP!VTI! +>Ref.D.CM.01.01CM_4412HAL.AY371157 +--ARASILSGGKLDAWEKIRLRPGGSKKYRLKHLIWASNELERFALNPGLLET-SDGCKQILGQLQP-ALKTGTEELRSLFNAVAVLYCVH-ERIEVKDTKEALDKIEEE-QNKSK---KKAQQA--AADTGDNK------QVSQNYPIVQNLQ-GQMVHQALSPRTLNAWVKVIEEKAFNPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVQAGPVAPGQMREPRGSDIAGTTSTLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QA--TAGMN--AA---IMMQRGNFKGPKRIVKCFNCGKEGHIAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSNKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEIA-PSQKQEQ-KD--KDQE-LYPLTSLKSLFGNDPLSQ*- +>Ref.F1.FR.96.96FR_MP411.AJ249238 +MGARASVLSGGKLDAWERIRLRPGGKKKYRMKHLVWASRELERFAVDPGLLET-PEGCKQIIRQLQP-SLQTGSEELRSLFNTVAVLYCVH-QKIEIKDTKEALEKLEEE-QNKGQ---QKTQQA--AADKG----------VSQNYPIVQNLQ-GQMVHQPISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPAHAGPILPGQMREPRGSDIAGTTSTLQEQIQWMTSN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQASQEVKNWMTESLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QA--T---N--AA---IMMQKSNYKGPRRFIKCFNCGKEGHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFKEEIT-PSPKQEQ-KD--EGQGLYPPLASLKSLFGSDP!VTI! +>Ref.A2.CY.94.94CY017_41.AF286237 +MGARASILSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELEKFSINPGLLET-PEGCRQIIRQLQP-ALQTGTEELKSLYNTVVVLYWVH-QRVDVKDTKEALDKIEEE-QNK-----QKTQHA--AADTGNSS--------SQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSD---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCRSILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMSHVQS--T---N--TN---IMMQRGNFRGQKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQSRT----------EPTAPPA-----------ENLRMGEEIT-SSLKQEL-ET--REP--YNPAISLKSLFGNDPLLQ*- +>Ref.H.CF.90.056.AF005496 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALNPGLLET-PEGCLQIIEQIQP-AIKTGTEELKSLFNLVAVLYCVH-RKIDVKDTKEALDKIEEI-QNKSQ---QKTQQA--AADKEKDN------KVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNAMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTGN---PAIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGQGASIEEMMTACQGVGGPSHKARVLAEAMS--QV--T---N--TNT-AIMMQKGNFKGQRKFVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEMT-PSPKQEQLKD--KE----PPLASLRSLFGSDPLLQ*- +>Ref.A2.CM.01.01CM_1445MV.GU201516 +--ARASVLSGGKLDAWEKIRLRPGGRKKYRMKHLVWASRELEKYSINPGLLET-SEGCKQIIRQLHS-ALPVGTEELKSLYNTIAVLYYVH-QKIEVKDTKEALDKLEEE-QNKYK---QKTQQA--AAATGNSS--------SQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QIHST---N--QN---VMMQRGNFRGPKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPPNKGRPGNFPQSRT----------EPTAPPA-----------ENVGMGEEIA-SSSKQEL-RN--REQ--HTPTISLRSLFGNDPLSQ*- +>Ref.A1.AU.03.PS1044_Day0.DQ676872 +MGARASILSGGRLDAWEKIRLRPGGKKKYRLKHLVWASRELERFAL?P?LLES-AEGCQQIMEQLQP-A?KTG?EEIKSLFNTVATLYCVH-QRIDVKDTKEA?DKIEEI-KNKSK---QRTQQA--AADTGNSG------KVSQNYPIVQNAQ-GQMI?QNLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNVMLNIVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQIREPRGSDIAGATSTPQEQLQWMTGN---PPIPVGDIYKRWIILGLNKIVRMYSPTSILDIRQGPKESFRDYVDRFFKALRAEQATQEVKSWMTETLLVQNANPDCKSILKALGSGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--Q---Q--TS---IMMQRGNFRGGQKRIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSSKGRPGNFPQSRP----------EPTAPPA-----------ELFGMGEEIT-SPPKQEQ-KD--KEQ--VPPLVSLKSLFGNDPSSQ*- +>Ref.J.SE.93.SE9280_7887.AF082394 +MGARASILSGGKLDDWEKIRLRPGGKKKYRIKHLVWASRELDRFALNPGLLES-AKGCQQILVQLQP-ALQTGTQEIKSLYNTVATLYCVH-QRIEIKDTMEALEKIEEI-QNKNK---QQAQKA--ETDKKDNS------QVSQNYPIVQNLQ-GQPVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTIGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIAPGQVREPRGSDIAGTTSTLQEQIGWMTGN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKALRAEQATQDVKNWMTDTLLVQNANPDCKTILKALGSGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--TN---IMMQRGNFRDHKRIVKCFNCGKQGHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESLGLGEEI--PSPKQEP-KD--KEL---YPLTSLKSLFGSDPLSQ*- +>Ref.F2.CM.95.95CM_MP257.AJ249237 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHIVWASRELKRFALNPGLLET-TEGCKKIIGQLQP-SLQTGSEELKSLFNTIVVLYYVH-QKIEVRDTKEALDKLQEE-QDKHQ---QKTQQA--TADKGVSK------GVSQNYPILQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPSHKARILAEAMS--KA--T---G--AA---IMMQKSNFKGQRRIVKCFNCGKEGHIARNCRAPRKRGCWK-CGQEGHQMKDCTERQANFLGKMWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIA-PSPKQEQ-KD--KEQ--VPPLISLKSLFGS!PVVTI! +>Ref.F2.CM.95.95CM_MP255.AJ249236 +MGARASVLSGGKLDAWEKIRLKPGGKKRYRLKHLVWASRELERFALNPSLLET-TEGCKKIIGQLQS-SLQTGSEELKSLYNAVVVLYYVH-QRIDVRDTKEALDKLQEE-QDKSQ---QKEQQK--AADKE----------VSQNYPIVQNIQ-GQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQITWMTGN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPGHKARILAEAMS--KA--T---S--TA---IMMQKSNFKGQKRIVKCFNCGKEGHIARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNRGRPGNFLQNRP----------EPTAPPA-----------ENFGFGEGIT-PSPKQEQ-KG--EEQ--APPLVSLKSLFGSDP!SRN! +>Ref.C.BR.92.BR025_d.U52953 +MGARASILRGGKLDAWERIKLKPGGKKHYMMKHLVWASRELERFALDPGLLET-SEGCKQIMKQLQP-ALQTGTKELISLHNTVATLYCVH-EKIDVRDTKEALDKIKEE-QNKSQ---QKTQQA-EAADKG---------KVSQNYPIVQNLQ-GQMVHQPISARTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLQEQITWMTNN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPGHKARVLAEAMS--KV--N---N--TN---IMMQRSNCKGPKRTIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQVKDCTERQANFLGKIWPSHRGRPGNLLQNRT----------EPTAPPE-----------ESFRFGEETTTPSRKQET-ID--KEL----PLTSLKSLFGSDPLST*- +>Ref.G.KE.93.HH8793_12_1.AF061641 +MGAR?S?LSGGKLDAWEKI?LTPGGKKKYRLKHLVWASREMERFALNPGLLET-AEGCQQIMSQLQP-AI?TGTEEIKSLFNTVATLYCVHP-KIEVKDTKEALEEVEKI-QKKSQ---QKIQQA--ARDEGNSS------QVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRIHPPQAGPIPPGQIREPRGSDIAGTTSNLQEQIRWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QA--T---G--AAA-AIMMQKSNFKGPKRNIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANF!GKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIA-PSPKPEP-KE--KEI---HPLASLKSLFGSDP!VTV! +>Ref.A2.CD.97.97CDKTB48.AF286238 +MGARASVLSGGKLEAWEKIRLRPGGKKKYRLKHLVWASRELEKFSINPSLLET-ETGCRRIFGQLQP-ALETGTEELRSLYNTIAVLYFVH-QKIEVKDTKEALDKIEEE-QNKCK---QKTQQA--AADTGSSSSQNYRGSSSQNYPIVQNAQ-GQMVHQAVSPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVQAGPIPPGQMREPRGSDIAGATSNLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKSILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--Q---N--TN---IMIQRGNFKGQKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQSRT----------EPTAPPM-----------E-----EEIT-SSLKQEN-RE--PST----PAISLKSLFGNDLLSQ*- +>Ref.G.BE.96.DRCBL.AF084936 +MGARASVLSGGKLDAWEKIRLRPGGKKRYRMKHLVWASRELDRFALNPGLLET-AEGCQKIMAQLQP-ALQTGTEEIKSLFNTVATLYCVH-QKIEVRDTKEALEEVEKI-QKKSQ---QKENSS--S-------------QVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKETINDEAAEWDRLHPQQAGPIAPGQIRDPTGSDIAGATSTLQEQIRWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKSWMTDTLLIQNANPDCKIILKGLGQGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--S---G--AAA-AIMMQKSNFKGPRRTIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKECTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ENFGFGEEIA-PSPKQEQ-KE--KEL---YPLSSLKSLFGN!PIVKV! +>Ref.K.CD.97.97ZR_EQTB11.AJ249235 +MGARASVLSGGKLDKWEKIQLRPGGKKKYRLKHLVWASRELERFALNPNLLET-VEGCRQIIRQLQP-SLQTGSEELRSLFNTVATLYWVH-QSIQVRDTKEALDKLEEE-QNRTQ---QKTQQG--KADKG----------VSQNYPIVQNLQ-GQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRMHPVQAGPIPPGQIREPRGSDIAGTTSTLQEQITWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFRVLRAEQATQEVKNWMTETLLVQNANPDCRTILKALGSGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SA---VMMQRGNFKGQRRIIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCSERQANFLGKFWPLNKERPGNFLQNRP----------EPTAPPA-----------ESFGFGEKIT-PSLRQEM-KD--QEQ--GPPLTSLKSLFGSDPLSQ*- +>Ref.D.TZ.01.A280.AY253311 +--ARASVLSGGQLDAWEKIRLRPGGKKKYQLKHIVWASRELERFALNPGLLET-SEGCKQI!---QP-AIQTGSEELKSLFNTVATLYCVH-RKIEVKDTKEALEKLEEE-QTKSK---KKAQQA--TADTGSSS------QVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIAWMTNN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---N--VNA-AIMMQRGNFKGPRKIIKCFNCGKEGHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------EIFGFGEEIK-PSQKQEQ-KDKDKEL---YPSASLKSLFGNDPLSQ*- +>Ref.F2.CM.02.02CM_0016BBY.AY371158 +--ARASVLSGGKLDDWEKIRLRPGGKKKYRLKHIVWASKELERFALNPGLLET-TEGCKQIIGQLQ-SSLQTGSEEIKSLYNTVAVLYYVH-QKIQIRDTKEALDKLQEE-QDKYQ---QKTQPA--AADKG----------VSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVQAGPIPPGQIREPRGSDIAGTTSTLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARILAEAMS--QV--T---A--TS---VLMQKSNFKGQKRIVKCFNCGKEGHIAKNCRAPRKRGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFIQSRP----------EPTAPPA-----------EGFGFGEEIT-PSPKQEQ-KD--KGL--YPPLTSLKSLFGNDP!VTI! +>Ref.F1.BE.93.VI850.AF077336 +MGARASILSGGKLDEWEKIQLRPGGKKRYKMKHLIWASRELERFALDPGLLET-SEGCQKIIRQLQP-SLQTGSEELKSLFNTVAVLYYVH-QRAGVTDTKEALDKLEEE-QNKSQ---QKTQQA--AADKG----------VSQNYPIVQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPTDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPAPPGQMREPRGSDIAGTTSTLQEQIQWMTGN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKVLRAEQASQDVKGWMTDTLLVQNANPDCKTILKALGTGATLEEMMTACQGVGGPSHKARVLAEAMS--QA------N--SA---IMMQKSNFKGQRRVVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSNKGRPGNFLQSRP----------EPTAPPA-----------ESFGFREEIT-PSPKQEQ-KD--GEL--YPPLASLKSLFGNDP!VTI! +>Ref.B.NL.00.671_00T36.AY423387 +MGARASVLSGGELDRWEKIRLRPGGKKRYKLKHIVWASRELERFAVNPGLLET-SEGCRQILGQLQP-ALQTGSEELKSLFNTVATLYCVH-ARIEVKDTKEALEKIEEE-QNKSKKRAQQAQQA--EADAGKNN------PVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNN---PPIPVGEIYKRWIILGLNKIVRMYSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNSNPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---S--AP--AIMMQRGNHRNQRRTVKCFNCGKEGHIARNCRAP?KKGCWK-C?K?GHQMKDCT?RQA?FLGKIWPSHKGRPGNFLQSRPEPTAPSQSRPEPTAPPE-----------ESFRFGEETTTPSQRQEP-TD--KEL---YPLASLKSLFGSDP!VTI! +>Ref.C.IN.95.95IN21068.AF067155 +MGARASILRGGKLDKWEKIRLRPGGKKRYMLKHLVWASRELDRFAVNPGLLET-AEGCKQIIKQLQP-ALQTGTEELRSLFNTVATLYCVH-AGIEVRDTKEALDKIEEE-QNKIK---QKTQQA--KEDDG---------KVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVPAGPIAPGQLREPRGSDIAGTTSTLQEQIAWMTNN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMS--Q---T---N--SA---ILMQRSNFKGSKRIVKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFRF-EETT-PAPKQEP-KD--RE-----PLTSLRSLFGSDPLSQ*- +>Ref.B.US.98.1058_11.AY331295 +----ASVLSGGKLDTWEKIRLRPGGKKKYKLKHIVWASRELERFALNPGLLET-AEGCRQLLGQLQP-SLQTGSEELKSLFNTIATLYCVH-QRIEVRDTKEALDKIEEE-QNKSK---KKAQQAAAAADTGNSS------QVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFAALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRIHPAQAGPIAPGQIRDPRGSDIAGTTSTLQEQITWMTNN---PPIPVGEIYKKWIIMGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SG--AIMMQKGNFRNQ--VVRCFNCGKVGHIAKNCRAPRKKGCWK-CGKEGHQMKDCDQRQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFRFGEETTTPSQKQEP-QE--------YPLASLRSLFGNDPSSQ*- +>Ref.J.CD.97.J_97DC_KTB147.EF614151 +--------------AWEKIWLRRRGEKKYRRKHIVWASRELDRYALNPGLL!S!AEGGEQILVQIQP!SL!TGAEEIKSLFNTEATLYCVH!!RIDIRDTKEALDKIEE!L!NKSK---EKAKKE--AVKKYNS-------QVSHNYPILQNM!!GELVHQALSPRTLNAWVKVIEEKGFNPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQIAWITGNGGNQPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILRALGAGATLEEMMTACQGVRVSSHRARVFGEAIS--QV--N---N--TN---IIMQRGNFRGQKRSVKCFNCGKEGHIAKNCRAPRKKGC!K!CGKEGHQIKNCTERQANFLGKVWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEKIT-PSQKQEP-R---KEL---YPSASLKSLFGSDPSSQ*- +>Ref.J.CM.04.04CMU11421.GU237072 +MGARASVLSGGKLDTWEKIRLRPGGKKRYRLKHLVWASRELDRFALNP?LLET-SKGCQQILVQLQP-SYQTGTEEIKSLYNTVATLYCVH-E?IEVKDTKE?LDKIEEL-QKKNK---QQAQKA--E?DK???S------QVSQNYPIVQNMQ-GQPV??ALSPRTLNAWVKV?E?KA?SPEVIPMFS?LSEGAT?QDLNTMLNT?GGH?AAMQMLKDTINEEAAEWDR?HPVHAGP?APGQAREPRGSDIAGTTSTLQEQIAWMTGN---PPIPVGEIYK?WIILGLNKI?RMYSPVSILDIRQGPK?PFR?YVDRFFKTLRAEQATQEVKNWMTDTLLIQNANPDCRT?LKALGPGATL?EMMTA?QGVGGPGHKARVL?EAMS--QM--T---N--TA--NIMMQ?G?FKG?KRMIKCFNC?KPGHL?R?CRAP??KGCWK-CGQEG?QMKDCTERQANFLG?IWPSN?GRPGNF?QS?P----------EPTAPPA-----------ESFGFGEE-T-??PKQEA-----KEL---YPLTSLKSLFG?DP?SQ*- +>Ref.H.GB.00.00GBAC4001.FJ711703 +MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELDRFALNPDLLET-ADGCLKI?GQIQP-ALQTGTEEIKSLFNLVAVLYCVH-QKIEVQDTSEALNKVKEI-QNKNQ---QTTQQA--TA?KEKDS------KISQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALS?G?TPQD?NTMLNSVGGHQAAMQ?LKDTINEEAAEWDRTHPVHAGPIPPGQMREPRGSDIAGTT?NLQEQIAWMT?N---PP?PV??IYKRWII?GLNKIVRMYSPVSILDIKQGPKEPFR?YVDR?FKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILKALGQGASIEEMMTACQGVGGPGHKARVLAEAMS--QM--T---N--MNT-AIMVQKGNFKGQRRTVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ECFGFGEEMT-PPPKQEM-KE--KE----PPLTSLRSLFGSDPLSQ*- +>Ref.G.NG.92.92NG083.U88826 +VGARASVLSGGKLDSWEKIRLRPGGRKKYKLKHIVWASRELGRFALNRDLLET-AEGCVQIMKQLQP!SL!TGTEELRSLFNTVATLYCVH-QKIEVKDTKEAPEEVEKI-QKNSQ---QEIQQA--AKNEGNSN------PVSQNYPIVQNAQ-GQMIHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINDEAAEWDRIHPQQAGPIPPGQIREPSGSDIAGTTSTLQEQIRWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--S---G--AAAAAIMMQKSNFKGPRRIIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKECTERQANFLGKIWPSNKGRPGNFLQNRT----------EPTAPPA-----------ESFGFGEEIA-PSPKQEP-KE--KEL---YPLTSLKSLFGSDP!VTV! +>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 +MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLET-SEGCRQILGQLQP-SLQTGSEELRSLYNTVATLYCVH-QRIEIKDTKEALDKIEEE-QNKSK---KKAQQA--AADTGHSN------QVSQNYPIVQNIQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNN---PPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SA--TIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRP----------EPTAPPE-----------ESFRSGVETTTPPQKQEP-ID--KEL---YPLTSLRSLFGNDPSSQ*- +>Ref.B.TH.90.BK132.AY173951 +MGARASVLSGGQLDRWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLET-SEGCRQILGQLQP-SLQTGSEELRSLYNTIAVLYCVH-QKIEVKDTKEALEKIEEE-QNKSK---KKAQQA--AANTENSS------QVSQNYPIVQNMQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHN---PPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SA--TIMMQKGNFRNQRKIVKCFNCGKEGHIARNCRAPRKKGCWR-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFRFGEETTTPSQKQET-ID--KEL---YPLTALKSLFGNDPSSQ*- diff -Nru bppsuite-0.6.2/Examples/Data/HIV1_REF_2010_gag_macse_DNA.fasta bppsuite-0.7.0/Examples/Data/HIV1_REF_2010_gag_macse_DNA.fasta --- bppsuite-0.6.2/Examples/Data/HIV1_REF_2010_gag_macse_DNA.fasta 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/Data/HIV1_REF_2010_gag_macse_DNA.fasta 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,78 @@ +>Ref.D.CD.83.ELI.K03454 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATAAATGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAGACTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATATGCACTTAATCCTGGCCTTTTAGAAACA---TCAGAAGGCTGTAAACAAATAATAGGGCAGCTACAACCA---GCTATTCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTACAT---AAAGGAATAGATGTAAAAGACACCAAGGAAGCTTTAGAAAAGATGGAGGAAGAG---CAAAACAAAAGTAAG---------AAAAAGGCACAGCAAGCA------GCAGCTGACACAGGAAACAACAGC------------------CAGGTCAGCCAAAATTATCCTATAGTGCAGAACCTACAG---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTGAACGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGCTAAAAGAGACCATCAATGAAGAAGCTGCAGAATGGGATAGGTTACATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGTAAC---------CCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATTGTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAGGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCAAACCCAGATTGCAAGACTATCTTAAAAGCATTGGGACCACAGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGGCCCAGCCATAAAGCAAGAGTTCTGGCTGAGGCAATGAGC------CAAGCA------ACA---------AATTCAGTTACTACA---------GCAATGATGCAGAGAGGCAATTTTAAGGGCCCAAGAAAAATTATTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCAAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAGA---TGTGGAAAGGAAGGACACCAACTAAAAGATTGCACTGAGAGACAGGCTAATTTTTTAGGGAGAATTTGGCCTTCCCACAAGGGAAGGCCGGGGAACTTTCTCCAAAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTTGGGGAAGAGATAACC---CCCTCTCAAAAACAGGAGCAG---AAAGAC------AAGGAACTG---------TATCCTTTAACTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCGCAATAA--- +>Ref.C.ET.86.ETH2220.U46016 +ATGGGTGCGAGAGCGTCAATATTAAGAGGCGAAAAATTAGATGCCTGGGAAAAAATTAAGTTAAGGCCAGGGGGAAAGAAACACTATATGCTGAAACACCTAGTCTGGGCAAACAGGGAGCTGGAAAAATTTGCACTTAACCCTGACCTTTTAGATACA---TCAGCAGGCTGTAAACAAATAATTAAACAGCTACAACCA---GCTCTTCAGACAGGAACAGAGGAACTTAAATCATTATTTAATACAGTGGCAACTCTCTATTGTGTACAT---CAAAAGATAGAGATAAAAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAA---CAAAACGAAAGTCAG---------CAAAAAACACAGCAGGCA---GGAGCAGCTGACAGAGGA---------------------------AAGGACAGTCAAAATTATCCTATAGTGCAGAATATGCAG---GGGCAAATGGTACATCAGCCCATATCAGCTAGAACTTTGAATGCATGGGTAAAAGTAGTAGAGGAAAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACAGCTTTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTGTTGCACCAGGCCAAATGAGAGACCCAAGGGGAAGTGACATAGCAGGAACAACTAGTACCCTTCAGGAACAAATAGCATGGATGACAGGGAAC---------CCACCTGTTCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGGCTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTTTAAAACCTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAAACCATTTTAAGAGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGCCCACAAAGCAAGAGTGTTGGCTGAGGCAATGAGC------CAAGTA------AAC---------AAT------ACAACC---------ATAATGATGCAGAAAAGCAATTTTAAGGGCCCTAAAAGAGCAATTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGTACCGAGAGACAGGCTAATTTTTTAGGGAGACTTTGGCCTTCCAACAAGGGAAGGCCAGGGAATTTCCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGAGAGTCTCAGACCAGAGCCAACAGCCCCACCACCAGAGAGCTTCAGGTTC---GAGGAAGCAACA---CCTTCTCCGAAGCAGGAGCTG---AAAGAC------AGGGAA---------------GCCTTAACTTCCCTCAAATCACTCTTTGGCAACGACCACTTGTTACAATAA--- +>Ref.C.ZA.04.04ZASK146.AY772699 +ATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAATTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTCAACCCTGGCCTTTTAGAAACA---TCAGAAGGCTGTAAACAAATATTGGCACAAATACAACCA---GCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACAT---AAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAG---CAAAACAAAAGTCAG---------CAAAAAACACAGCAGGCA---AAAGCGGCTGACGAA------------------------------AAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTCAA---GGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAAGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAACACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGGCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAAC---------CCACCTATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCCCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAGCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGC------CAAATA------AAC---------AAT------GGAAAC---------ATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGCAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGGGAGGCCAGGGAATTTTCTCCAGAACAGACTA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCAGGTTC---GAGGAGACGACC---CCTGCTCCGAAACAGGAGCTG---AAAGAC------AGGGAA---------------CCTTTAACTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTCTCAATAA--- +>Ref.A1.UG.92.92UG037.AB253429 +ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTAGCCTTTTAGAAACA---ACAGAAGGATGTCAACAAATAATGGAACAATTACAATCA---GCTCTCAGAACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGCGTACAT---CAACGGATAGAGGTAAAAGACACCAAGGAAGCTCTAGATAAAATAGAGGAGATA---CAAAAGAAAAGCAAG---------CAAAAGACACAGCAGGCA------GCAGCTGACACAGGAAGTAGCAGC------------------AAGGTCAGCCAAAATTACCCTATAGTGCAAAATGCACAA---GGGCAAATGATCCACCAGTCCTTGTCACCTAGGACTTTGAATGCATGGGTGAAAGTAATAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTGAATATGATGCTGAACATAGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGCTACATCCAGTACATGCAGGGCCTGTTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCCTCAAGAACAAATAGCATGGATGACAGGCAAC---------CCACCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTAGATATAAAACAAGGGCCAAAAGAACCCTTCAGAGACTATGTAGATAGGTTTTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAGGTTGGATGACAGAAACATTACTGATCCAAAATGCAAATCCAGATTGTAAATCCATCCTAAGAGCATTAGGAGCAGGGGCTACATTAGAAGAAATGATGACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGT------CAAGTA------CAA---------CAT------ACAAAC---------ATAATGATGCAGAGAGGCAATTTTAAGGGCCAGAAAAGG---ATTAAGTGTTTCAACTGTGGCAAAGAAGGACATCTAGCCAAAAATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAGGGAAGGGCACCAAATGAAGGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCCTCAGAGCAGACCA------------------------------GAACCAACAGCCCCACCAGCAGCA------------------------------GAGATCTTTGGGATGAGGGAAGAGATAGTC---TCCCCTCCGAAGCAGGAGCAG---AACGAC------AGGGACCAG------AACCCACCTTCAGTTTCCCTCAAATCACTCTTTGGCAACGACCTCTTGTCACAGTAA--- +>Ref.A1.RW.92.92RW008.AB253421 +ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTGGCCTTTTAGAAACA---ACAGAAGGATGTCAAAAAATAATAGAACAGTTACAACCA---TCTGTCAAGACAGGAACAGAAGAACTTAAATCATTATTTAATACAGTAGCAACCCTCTATTGCGTACAT---CAACGGATAGATGTAAAAGACACCAAGGAAGCCCTAGATAAAATAGAGGAAATG---CAAAATAAGAGCAAG---------CAAAAGACACAACAGGCA------GCAGCTGACATAGGAAATAGCAGC------------------AAGGTCAGCCAAAATTACCCTATAGTGCAAAATGCACAA---GGGCAAATGATATATCAGTCCATGTCACCTAGGACTTTGAATGCATGGGTGAAAGTAATAGAAGAAAAGGGTTTCAACCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATATGATGCTAAACATAGTGGGGGGACATCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGACTGGGACAGGTTACATCCAGTACAGGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCCTCAAGAACAAATAGGATGGATGACAAGCAAC---------CCACCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGATGTAAAACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAATTCTCAGAGCTGAACAAGCTACACAGGATGTAAAACATTGGATGACAGAAACATTGCTGATCCAAAATGCAAATCCAGATTGTAAGTCCATTTTAAGAGCATTAGGAACAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTAGCTGAGGCAATGAGT------CAAGTA------CAA---------CAT------CCAAAC---------ATAATGATGCAGAGAGGCAATTTTAGGGGCCAGAAAAGG---ATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAGGGGAGGCCAGGAAATTTTCCTCAGAGCAGACCG------------------------------GAGCCATCAGCCCCACCAGCA---------------------------------GAGATCTTTGGGATAGGGGAAGAGATAGCC---TCCCCTCCGAAGCAGGAGCAG---AAAGAC------AGGGAACCG------GCCCAACCTTTAGTTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAGTAA--- +>Ref.H.BE.93.VI997.AF190128 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACGATTAGATACTTTGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATATAGTATGGGCAAGCAGAGAGCTGGAAAGATTTGCACTTAACCCCGGCCTTTTAGAATCA---GCAGAAGGCTGTCTACAAATAATAGAACAACTACGGCCA---TCTATTAAGACAGGAACAGAAGAACTTCWATCATTATTTAATACCGTAGCGACCCTCTATTGCGTACTT---CAAAGAATAGAGGTAAAAGACACCAAGGAAGCTTTAGGGAAGATAGAGGAAATA---CAAAACAAAAGGCAG---------CAAAAAACACAGCAAGCA------ACAGCTAATAAGGAAAGAGACAAC------------------AAGGTCAGTCAAAATTATCCTATAGTACAGAATGCTCAA---GGGCAGATGGTACACCAGCCCATATCACVTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAGGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAGGCAAT---------CCAAGTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAGATAGTAAGAATGTATAGTCCTGTTAGTATTCTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTTTAAGAGCTGAGCAAGCCACACAGGAGGTGAAGAATTGGATGACAGACACCTTGTTGGTCCAGAATGCAAATCCAGATTGCAAGACTATTTTAAGAGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AAT------GCAAATGCA---GCCATAATGATGCAGAAAAGCAACTTTAAGGGCCCAAGAAAAATTGTTAAATGTTTCAATTGTGGCAAAGAGGGACACATAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAGGGAAGGACATCAGATGAAGGACTGCACAGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCTCCAGAGCAGGCCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATGACC---TCCTCCCCGAAGCAGGAGCTG---AAGGAC------AAGGAA------------CCTCCCTTTGCTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAGTAA--- +>Ref.H.BE.93.VI991.AF190127 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGGCTAAAACATCTGGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGACCTTTTAGAAACA---GCAGATGGCTGCCAACAAATACTAGGACAGCTACAGCCA---GCTCTTAAGACAGGAACAGAAGACCTTCAATCATTATATAATACAATAGCAGTCCTCTATTGCGTACAT---CAAAGAATAGATGTGAAAGACACCAAGGAAGCTTTAGGGAAGATAGAGGAAATA---CAGAATAAGAACAAG---------CAAAGAACACAGCAGGCCCCAGCAGCAGCTGATAAAGAAAAGGACAGC------------------AAGATCAGTCAAAATTATCCTATAGTACAGAATGCCCAG---GGGCAAATGGTACACCAGGCAATATCACCTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAGTAGCATGGATGACAGGCAAT---------CCCCCAATTCCAGTGGGAGACATCTATAAGAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGACCAAAAGAACCCTTCAGAGACTATGTAGACAGGTTCTTTAGAGTTTTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAACTGGATGACAGACACCTTGTTGGTCCAAAATGCGAATCCAGATTGCAGGACTATTTTAAAAGCATTAGGACGAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCAAGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AAT------GCAAGTGCA---GCCATAATGATGCAGAAAGGCAACTTTAAGGGCCCAAGAAGAACTGTTAAATGTTCCAACTGTGGCAAAGAAGGACACATAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGACAGGAAGGACACCAGATGAAAGACTGCACAGGAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAGGGAAGGCCAGGGAATTTCCCCCAGAAGAGGCTA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAGATCACC---CCCTCTCCGAGGCAGGAGCTG---AAAGAA------CAGGAA------------CCTCCTTTAACTTCCCTCAGATCACTCTTTGGCAAC!GACCAATAGTCACAGTA!!A +>Ref.G.PT.x.PT2695.AY612637 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTTGCACTCAACCCTGACCTTTTAGAAACA---GCAGAAGGTTGTCAACAAATAATGAGACAGTTACAACCA---GCTCTCCAGACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAACACTCTATTGTGTACAT---CAAAGGATAGAGGTAAAAGACACCAAAGAAGCTCTAGAGGAAGTGGAAAAGACA---CAGAAGAAAAGT------------CAGAAACAACAGCAGGCA------GCAATGGACGAAGGAAACAGCAGC------------------CAAGTCAGCCAAAATTATCCTATAGTGCAGAATGCACAA---GGGCAAATGGTACATCAGGCCATATCACCCAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACACAGTAGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATTAATGAGGAAGCTGCAGAGTGGGACAGGATACATCCACAACAGGCAGGGCCTATCCCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTGCAGGAACAAATAAGATGGATGACCAGCAAT---------CCACCTATCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGATATAAGACAAGGGCCAAAAGAACCTTTTAGAGATTATGTAGATAGGTTCTTTAAAACTTTAAGAGCTGAACAAGCTACACAGGAAGTAAAAGGCTGGATGACAGACACCTTGCTGGTCCAAAATGCGAACCCAGATTGTAAGACCATCTTAAGAGCATTAGGACCAGGAGCTTCACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGTCACAAAGCAAGAGTTTTAGCTGAGGCAATGAGC------CAGGCA------TCA---------GGG------GCAACA---------ATAATGATGCAAAAAAGCAACTTTAAGGGTCCAAAAAGAATGATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACACCAAATGAAAGACTGCACAGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTTCTCCAGAACAGGCCC------------------------------GAGCCAACAGCCCCACCCGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAGATAGCC---CCCTCCCCGAAGCAAGAGCCG---AAGGAC------AAGGAGTTA---------TACCCCTTAACCTCCCTCAAATCACTCTTTGGCAGCGACCCC!TAGTCACAGTA!!A +>Ref.K.CM.96.96CM_MP535.AJ249239 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAGATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAAACTGAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTCAACCCTGGCCTTTTAGAGACA---ACAGAAGGCTGTCGGCAAATAATAACACAAATACAGCCA---TCCATTCAAACAGGATCAGAAGAGATTAAATCACTATATAATACAATAGCAGTCCTCTATTTTGTACAT---CAAAAGATAGAGGTAAAAGACACCAAGGAAGCCTTAGACAAACTAGAGGAAGAA---CAAAACAAAAGTCAG---------CGAAAGACACAACAAGAA------GCAGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTGCAG---GGGCAAATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTGAAGGTAATAGAGGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACTCCACAAGATCTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATGATGAAGCTGCAGAATGGGACAGGTTACACCCAGTGCATGCAGGGCCTATCCCACCAGGCCAAATGAGAGAACCGAGGGGGAGTGACATAGCAGGAACTACCAGCACCCTTCAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTGGGGGAAATCTATAAAAGATGGATAATCCTGGGTTTAAACAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAACCCTAAGAGCTGAACAAGCCACACAGGAAGTAAAGAATTGGATGACAGACACCCTGTTGGTCCAAAACGCAAACCCAGATTGTAAGACCATTTTAAAAGCGTTGGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGGGAGTGGGAGGGCCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATGAGC------CAGGTA------ACA---------AAT------CCAGTT---------GTAATGATGCAGAAAGGCAACTTTAAGGGCCATAGAAAAATTGTTAAGTGCTTCAACTGTGGCAAAGAAGGGCACATAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGGAAGGAAGGACATCAGATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATAACC---CCCTCTCCGAGGCAGGAGACC---AAAGAC------AAGGAACAG------AGCCCTCCTTTAACTTCCCTCAAATCACTCTTTGGCAACGACCCATTGTCACAATAA--- +>Ref.F2.CM.97.CM53657.AF377956 +---------AGAGCGTCACTATTAAGCGGGGGAAAATTAGATGATTTGGAAAAAATTCGGTTAAGGCCAGGGGGGAAGAAAAAATATAGGCTGAAACATATAGTATGGGCAAGCAGGGAGCTAGAAAGATTTGCACTTAATCCTGGCCTTTTAGAGACAAAG---GAAGGCTGTAAACAAATAATAGGACAACTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTTAAATCATTATTCAACACAATAGTAGTCCTCTATTATGTACAT---CAAAGGATAAAAATAGGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGACAAAAGTCAG---------CAAAAAACACAACCAGCA------GCGGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCAGGCAGGACCCATCCCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTACTAGCAACCTACAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAAGGCTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGATCATTTTAAAAGGATTAGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGGGTGGGGGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------TCT------ACATCC---------ATATTGATGCAGAAAAGCAACTTTAAGGGCCAAAGAAGAAATGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAAAATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCTGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAAAGCTTCGGGTTCGGAGAAGAGATAACT---CCCTCCCCGAAGCAGGAGCAG---AAAGAC------AAGGAAATG------TACCCTCCCTTGACTTCCCTCAAATCACTCTTTGGCAACGACCCT!TAGTCACAATA!!A +>Ref.F1.FI.93.FIN9363.AF075703 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAACTAGATGCATGGGAAAAAATTCGGTTAAGGCCGGGGGGAAAGAAACAATATAGAATAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCAATAGATCCTGGCCTTCTAGAAACA---TCAGAAGGCTGTCAAAAAATAATAGCACAGATACAGCCA---TCCATTCAGACAGGATCAGAAGAGCTTAGATCATTATATAACACAATAGCAGTCCTCTATTTTGTACAT---CAAAAGATAGAGGTAAAGGACACCAAGGAAGCTTTAGATAAGCTAGAGGAAGAA---CAAAACAAAAGTCAG---------CAAAAGACACAGCAAGCGGCAGCTGCAGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACATCAGGCTATATCACCTAGAACTTTAAATGCATGGGTAAAGGTGATAGAAGAGAAGGCTTTTAGCCCAGAAGTTATACCCATGTTTTCAGCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATTAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGACCTATTCCACCAGGCCAGATGAGGGAACCTAGGGGAAGCGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACAAGTAAC---------CCACCTGTCCCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGGATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAGCTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGACACCTTGTTGGTCCAAAATGCGAATCCAGATTGTAAGATCATTTTAAAAGGATTGGGAATAGGGGCTACACTAGAAGAAATGATGACAGCATGTCGGGGAGTGGGAGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATGAGC------CAAGCA------------------AAT------ACAACC---------ATAATGATGCAGAAAAGTAATTTTAGGGGCCAAAGAAGAATTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGAAATTGCAGGGCCCCCAGGAAAAAGGGCTGTTGGAAA---TGTGGACAAGAAGGGCACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTCCTTCAGAGTAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAGCCTCGGGATCAGAGAAGAGGTAACT---CCCTCTCCGAGGCAGGAGCAG---AAAGAA------GAGGGACAG------TACCCTCCCTTAGCTTCCCTCAAATCACTCTTTGGCAACGACCCC!TAGTCACAATA!!A +>Ref.D.UG.94.94UG114.U88824 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGAGGAAAATTAGATGAATGGGAAAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCACTTAATCCTGGCCTTTTAGAAACA---TCAGAAGGCTGTAGACAAATAATAAGACAGCTACAACCA---TCTATTCAGACAGGATCAGAGGAAATTAAATCATTATATAATACAGTGGTAACCCTCTATTGTGTACAT---GAGAGGATAAAGGTAGCAAGCACCAAGGAAGCTTTAGACAAGATAGAGGAAGAA---CAAGCCAAAAGTAAG---------AAAAAAGCACAGCAAGCA------ACAGCTGACACAAGAAACAGCAGC------------------CAGGTCAGCCAAAATTATCCTATAGTGCAAAACCTACAG---GGGCAAATGGTACACCATCCCCTATCACCTAGAACTTTGAACGCATGGGTAAAAGTAATAGAGGAGAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAGGATACCATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTGTTGCACCAGGCCAATTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTAACCTTCAGGAACAAATAGGATGGATGACAAGCAAT---------CCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACTGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAAACTATCTTAAAAGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGCA------ACA---------AAT------GCAAATACT---GCTATAATGATGCAGAGAGGCAATTTTAAGGGCCCAAAGAAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGGCACACGGCAAAAAATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAGGGAAGGACACCAAATGAAAGATTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAATGGAAGGCCAGGGAATTTCCTTCAGAGCAGACCC------------CCAGCA------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGATCTTCGGATTAGGGGAGGAGATAACA---CCTCCTCAGAAACAGGAGCAG---AAAGAC------AAGGAACTG---------TATCCTTTAACCTCCCTCAAATCACTCTTTGGCAACGACCCGTTGTCACAGTAA--- +>Ref.F1.BR.93.93BR020_1.AF005494 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAAAAAATTCGGTTAAGGCCGGGGGGAAAGAAAAAATATAGACTAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCAGGCCTTCTAGAAACA---TCAGAAGGCTGTCGAAAAATAATAGGACAGTTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTCAAATCATTATATAATACAATAGCAGTCCTCTATTATGTACAT---CAAAAGGTAGAGGTAAAAGACACCAAGGAGGCTTTAGAGAAGCTAGAGGAAGAA---CAAAACAAAGGTCGG---------CAAAAGACACAGCAAGCG------ACTGCTGAAAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACACCAGTCTTTATCACCTAGAACTTTAAATGCATGGGTAAAGGTGATAGAAGAGAAGGCTTTTAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGTTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAGGCTGCAGAATGGGACAGATTACATCCAACACAGGCAGGACCCATCCCCCCAGGTCAGATAAGGGAACCTAGGGGAAGTGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACAGGCAAC---------CCACCTGTCCCAGTGGGAGAAATGTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCGGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACCCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCATTGGGACCAGGGGCTACACTAGAGGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGCA------ACA---------AAT------ACAGCT---------ATAATGATGCAGAAAAGTAACTTTAAGGGCCAAAGAAGAATTGTTAAATGCTTTAATTGTGGCAAAGAAGGACACATAGCCAAAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAG---TGTGGAAGAGAGGGACACCAAATGAAGGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAACTTCATCCAGAACAGGCCA------------------------------GAGCCGTCAGCCCCGCCAGCA---------------------------------GAGAGCTTCAGGTTCGGGGAGGAGACAACC---CCATCTCCGAAGCAGGAGCAG---AAAGAC------GAGGGACTG------TACCCTCCCTTAGCTTCCCTCAAATCACTCTTTGGCAACGACCCC!TAGTCACAATA!!A +>Ref.D.CM.01.01CM_4412HAL.AY371157 +------GCGAGAGCGTCAATATTAAGCGGGGGAAAATTGGATGCATGGGAAAAAATTCGGTTACGGCCAGGGGGAAGCAAAAAGTATAGGCTAAAACATCTAATATGGGCAAGCAATGAGCTAGAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---TCAGATGGCTGTAAACAAATACTAGGCCAGCTACAACCA---GCTCTTAAAACAGGAACAGAAGAACTTAGATCATTATTTAATGCAGTAGCAGTACTCTATTGTGTACAT---GAAAGGATAGAGGTAAAGGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAA---CAAAACAAAAGTAAG---------AAAAAAGCACAGCAAGCA------GCAGCTGACACAGGGGACAACAAA------------------CAGGTCAGCCAAAATTATCCTATAGTGCAGAACTTACAG---GGGCAAATGGTACACCAAGCCCTATCACCCAGAACCTTGAACGCATGGGTAAAAGTAATAGAGGAAAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAGGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGACAGGCTACATCCAGTGCAAGCAGGGCCTGTTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATTGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGGTGGATGACAAGTAAT---------CCACCAATCCCAGTAGGGGAAATCTATAAAAGATGGATAATCTTGGGATTGAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAGACAAGGACCAAAAGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGAAACCTTGTTGGTTCAAAATGCAAACCCAGACTGTAAAACTATCTTAAAGGCGTTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGGCCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGCA------ACAGCAGGTATGAAT------GCTGCA---------ATAATGATGCAGAGGGGCAATTTTAAGGGCCCAAAGAGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGGCACATAGCAAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAGAGAAGGACACCAAATGAAAGATTGCACAGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGAAGGCCAGGGAACTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATAGCC---CCCTCTCAGAAACAGGAGCAG---AAAGAC------AAAGACCAGGAA---CTGTATCCTTTAACTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAA--- +>Ref.F1.FR.96.96FR_MP411.AJ249238 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAGAATTCGATTAAGACCGGGGGGAAAGAAAAAATATAGAATGAAGCATCTAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCAGTTGATCCTGGACTTCTAGAAACA---CCAGAAGGCTGTAAGCAAATAATAAGACAGCTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTTAGATCATTGTTCAATACAGTAGCAGTTCTCTATTGTGTACAT---CAAAAGATAGAGATAAAGGACACCAAGGAAGCTTTAGAGAAGTTAGAGGAGGAA---CAAAACAAAGGTCAG---------CAAAAGACACAGCAAGCG------GCAGCTGACAAAGGA------------------------------GTCAGTCAAAATTACCCTATAGTACAAAATCTTCAG---GGACAGATGGTACATCAGCCTATATCACCTAGAACTTTAAATGCATGGGTAAAAGTGATAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAATACAGTGGGTGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGCGCATGCAGGGCCTATCCTACCAGGCCAGATGAGAGAACCTAGGGGTAGTGACATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACAAGCAAC---------CCACCTGTCCCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAGACAAGGGCCAAAGGAACCTTTTAGAGACTATGTGGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAGAATTGGATGACAGAAAGCTTGCTGGTGCAAAATTCGAACCCAGACTGTAAGACCATCTTAAAAGCATTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAGGCAAGGGTTTTGGCTGAGGCCATGAGC------CAAGCA------ACA---------AAT------GCAGCT---------ATAATGATGCAGAAAAGTAACTATAAGGGCCCAAGAAGATTTATTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAAAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAAGAAGGACATCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTTCTTCAGAACAGGCCA------------------------------GAGCCAACAGCCCCGCCAGCG---------------------------------GAGAGCTTCGGGTTCAAAGAGGAAATAACC---CCCTCTCCGAAGCAGGAGCAG---AAGGAC------GAGGGACAGGGACTGTATCCTCCCTTAGCCTCCCTCAAATCACTTTTTGGCAGCGACCCT!TAGTCACCATA!!A +>Ref.A2.CY.94.94CY017_41.AF286237 +ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATTTGGTATGGGCAAGCAGGGAGCTGGAGAAATTCTCAATTAACCCTGGCCTTTTAGAAACA---CCAGAGGGATGTAGACAAATAATAAGGCAGTTACAACCA---GCTCTCCAAACAGGAACAGAAGAACTTAAATCATTATATAATACAGTAGTAGTCCTCTACTGGGTACAT---CAAAGGGTAGATGTAAAAGACACCAAGGAAGCTCTAGATAAAATAGAGGAAGAA---CAAAACAAG---------------CAGAAAACACAGCATGCA------GCAGCTGACACAGGGAACAGCAGC------------------------AGTCAAAATTATCCCATAGTGCAAAATGCACAA---GGGCAAATGGTACACCAGGCTATATCACCTAGGACGTTGAATGCCTGGGTCAAAGTAGTAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCTATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGTTGGATGACCAGCGAT---------CCACCCATCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCCACACAGGAGGTAAAAAACTGGATGACGGACACCTTGCTGGTCCAAAATGCGAACCCAGATTGTAGATCCATCTTGAGAGCATTAGGACCAGGGGCCTCATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTGGCTGAAGCAATGAGCCATGTACAAAGT------ACA---------AAT------ACAAAC---------ATAATGATGCAGAGAGGCAATTTTAGGGGTCAAAAAAGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAA---TGTGGAAAGGAAGGACATCAAATGAAAGATTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAAGGGAGGCCAGGAAATTTTCCTCAGAGCAGAACA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAACTTGAGAATGGGGGAAGAGATAACC---TCCTCCCTGAAGCAGGAACTG---GAGACC------AGGGAACCA------TACAATCCTGCAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTTACAGTAA--- +>Ref.H.CF.90.056.AF005496 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATGCTTGGGAGAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGGCCTTTTAGAAACA---CCAGAAGGCTGTCTACAGATAATAGAACAGATACAGCCA---GCTATTAAGACAGGAACAGAAGAACTTAAATCATTATTTAATCTAGTAGCAGTCCTCTATTGCGTACAT---CGAAAAATAGATGTGAAAGACACCAAGGAGGCTTTAGATAAGATAGAGGAAATA---CAAAACAAAAGTCAG---------CAAAAAACACAGCAAGCA------GCAGCTGATAAGGAAAAAGACAAC------------------AAGGTCAGTCAAAATTATCCTATAGTACAGAATGCTCAA---GGGCAGATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTGCATGCAGGGCCTATTCCACCAGGCCAAATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTACTAGTACCCTGCAGGAACAAATAGCATGGATGACAGGCAAT---------CCAGCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAGATAGTAAGAATGTATAGTCCTGTCAGCATTCTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTTTTTAAAACTTTAAGAGCTGAGCAAGCCACACAGGATGTGAAGAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCAAATCCAGATTGCAAGACTATATTAAGAGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AAT------ACAAATACA---GCCATAATGATGCAGAAAGGCAACTTTAAGGGCCAAAGAAAATTTGTTAAATGCTTCAACTGTGGCAAAGAGGGACACATAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAGAGAAGGACATCAGATGAAAGACTGCACAGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCTCCAGAGCAGGCCA------------------------------GAACCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAGATGACC---CCCTCTCCGAAGCAGGAGCAGCTGAAGGAC------AAGGAA------------CCTCCCTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTTACAGTAA--- +>Ref.A2.CM.01.01CM_1445MV.GU201516 +------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGAATGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATACTCAATCAACCCTGGTCTTTTAGAAACA---TCGGAAGGATGTAAACAAATAATAAGGCAGTTACATTCA---GCTCTCCCAGTAGGAACAGAAGAACTTAAATCACTATATAATACAATAGCAGTCCTCTACTATGTACAT---CAAAAAATAGAGGTAAAAGACACCAAGGAAGCCCTAGATAAATTAGAGGAGGAG---CAAAACAAATACAAG---------CAGAAGACACAGCAGGCA------GCAGCTGCCACAGGAAATAGCAGC------------------------AGTCAGAATTATCCCATAGTGCAAAATGCACAA---GGGCAAATGGTGCACCAGGCCATATCGCCTAGGACTTTGAATGCATGGGTCAAAGTAGTAGAAGAAAAAGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACTATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAGGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACCAGCAAC---------CCACCTATCCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCCAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAACTCTCAGAGCTGAACAAGCTACACAGGATGTAAAAAATTGGATGACAGACACCTTGCTGGTCCAAAATGCGAACCCAGATTGTAAAACTATCCTGAGAGCGTTAGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTCTTGGCTGAAGCAATGAGC------CAAATACACAGTACA---------AAT------CAAAAT---------GTAATGATGCAGAGAGGCAATTTTAGAGGTCCAAAAAGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGTTGCTGGAAA---TGTGGGAAGGAAGGACATCAAATGAAAGATTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTCCCAACAAAGGGAGGCCAGGAAACTTTCCCCAGAGCAGAACA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAACGTTGGAATGGGGGAAGAGATAGCT---TCCTCGTCGAAGCAGGAACTG---AGAAAC------AGGGAACAA------CACACTCCTACAATTTCCCTCAGATCACTCTTTGGCAACGACCCCTTGTCACAGTAA--- +>Ref.A1.AU.03.PS1044_Day0.DQ676872 +ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAGATTAGATGCATGGGAGAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGAGAGATTCGCACTTAAYCCTRGCCTTTTAGAATCA---GCAGAAGGATGTCAACAAATAATGGAACAGTTACAACCA---GCTCTYAAGACAGGAWCAGAAGAAATTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTACAT---CAAAGGATAGATGTAAAAGACACCAAGGAAGCTYTAGATAAAATAGAGGAAATA---AAAAATAAGAGCAAG---------CAAAGGACTCAACAGGCA------GCAGCTGACACAGGAAACAGCGGC------------------AAGGTCAGCCAAAATTACCCTATAGTGCAAAATGCACAG---GGGCAAATGATACAYCAAAACTTGTCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTTAGTCCAGAAGTGATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATGTAATGCTGAACATAGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGACACCATCAATGAAGAAGCTGCAGAATGGGACAGGTTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGACATAGCAGGAGCTACTAGTACCCCTCAAGAACAATTACAATGGATGACAGGCAAC---------CCACCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACTAGCATTTTGGATATAAGACAAGGGCCAAAAGAATCCTTCAGAGACTATGTAGATAGGTTCTTTAAAGCTCTTAGAGCTGAGCAAGCTACACAGGAGGTAAAAAGTTGGATGACAGAGACATTACTGGTCCAAAATGCAAATCCAGATTGTAAGTCCATTCTAAAAGCATTAGGATCAGGAGCTACATTAGAAGAAATGATGACAGCATGCCAGGGAGTGGGAGGACCCAGCCATAAGGCAAGGGTTTTGGCTGAAGCAATGAGT------CAAGCA------CAA---------CAA------ACAAGC---------ATAATGATGCAGAGAGGCAACTTTAGGGGCGGCCAGAAAAGGATTAAGTGTTTTAACTGTGGCAAAGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGGAAGGAGGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAGGGGAGGCCAGGAAATTTCCCTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCG---------------------------------GAGCTCTTTGGGATGGGGGAAGAGATAACC---TCCCCTCCGAAGCAGGAGCAG---AAGGAC------AAGGAACAG------GTCCCACCCTTAGTTTCCCTCAAATCACTCTTTGGCAACGACCCATCGTCACAGTAA--- +>Ref.J.SE.93.SE9280_7887.AF082394 +ATGGGTGCGAGAGCGTCAATATTAAGTGGGGGAAAATTAGATGATTGGGAAAAAATTCGGTTGAGGCCAGGGGGGAAGAAAAAATATAGGATAAAGCATCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTTCTAGAGTCA---GCAAAAGGCTGTCAACAAATACTAGTACAGCTCCAACCA---GCTCTCCAGACAGGAACACAAGAAATTAAATCATTGTATAATACAGTAGCAACCCTCTATTGCGTACAT---CAGAGGATAGAAATAAAAGACACCATGGAAGCTTTAGAGAAGATAGAGGAAATT---CAAAACAAGAACAAA---------CAGCAGGCACAGAAAGCA------GAAACTGACAAAAAAGACAACAGT------------------CAGGTCAGTCAAAATTATCCTATAGTGCAGAATCTGCAA---GGGCAACCGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTGATAGAAGAAAAAGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACACAATAGGGGGACACCAAGCAGCTATGCAAATGTTAAAAGATACTATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATTGCACCAGGCCAGGTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTCCAGGAACAAATAGGATGGATGACAGGCAAT---------CCACCTATCCCAGTAGGAGAGATTTATAAAAGATGGATAATTCTGGGACTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAGACAAGGACCAAAAGAACCTTTTAGAGACTATGTAGACAGGTTCTTTAAAGCTCTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAATTGGATGACAGATACCTTGCTGGTCCAAAATGCAAATCCAGATTGCAAGACCATTTTAAAAGCATTAGGATCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGTCATAAGGCGAGAGTTTTGGCTGAAGCAATGAGC------CAAGTG------ACC---------AAT------ACCAAC---------ATAATGATGCAAAGAGGTAACTTTAGGGACCATAAAAGAATTGTTAAGTGTTTCAATTGTGGCAAACAAGGACACATAGCAAAAAACTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAGATTTGGCCTTCCAGCAAAGGGAGGCCAGGGAACTTTCTCCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCCTCGGGCTCGGAGAGGAGATC------CCCTCCCCGAAACAGGAGCCG---AAGGAC------AAGGAACTG---------TATCCTCTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCACAATAA--- +>Ref.F2.CM.95.95CM_MP257.AJ249237 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTAAGGCCGGGGGGGAAGAAAAAATATAGGCTGAAACATATAGTATGGGCAAGCAGGGAGCTAAAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---ACAGAAGGCTGTAAGAAAATAATAGGACAACTACAACCA---TCCCTTCAGACAGGGTCAGAGGAACTGAAATCATTATTTAACACAATAGTAGTTCTCTATTATGTACAT---CAAAAGATAGAGGTAAGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGACAAACATCAG---------CAAAAAACACAACAAGCA------ACGGCTGACAAAGGGGTCAGTAAA------------------GGGGTCAGTCAAAATTACCCTATACTACAAAATCTTCAG---GGGCAAATGGTACACCAGAGTCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGACCTATCCCACCAGGTCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACCACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCCACGCAGGAAGTAAAAGGCTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCATTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGTGTGGGAGGACCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATGAGC------AAAGCA------ACA---------GGT------GCAGCC---------ATAATGATGCAGAAGAGCAACTTTAAGGGCCAAAGAAGAATTGTTAAGTGTTTTAACTGTGGCAAAGAAGGACATATAGCTAGAAATTGCAGGGCCCCTAGAAAAAGGGGCTGCTGGAAA---TGTGGACAGGAAGGACACCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATGTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATAGCT---CCCTCCCCGAAGCAGGAGCAG---AAAGAC------AAGGAACAG------GTTCCTCCCTTGATTTCCCTCAAATCACTCTTTGGCAGC!GACCAGTAGTCACAATA!!A +>Ref.F2.CM.95.95CM_MP255.AJ249236 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTAAAGCCGGGGGGAAAGAAAAGATATAGGCTAAAACATCTAGTATGGGCAAGCAGGGAACTAGAACGATTTGCACTTAATCCTAGCCTTTTAGAAACA---ACAGAAGGCTGTAAGAAAATAATAGGACAATTACAATCA---TCCCTTCAGACAGGATCAGAAGAGCTTAAATCACTATACAATGCAGTAGTAGTTCTCTATTATGTACAT---CAAAGGATAGATGTAAGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGATAAAAGTCAG---------CAAAAGGAACAACAAAAG------GCGGCTGACAAAGAG------------------------------GTCAGTCAAAATTACCCTATAGTGCAGAATATTCAG---GGGCAAATGGTACACCAGGCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATGAGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTATCCCACCAGGGCAGATGAGAGAACCTAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAACATGGATGACAGGCAAC---------CCACCCGTCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAACAAGCTACACAGGAGGTAAAAAACTGGATGACAGAAACCTTGTTGGTCCAAAATTCGAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAATTCTGGCTGAGGCAATGAGC------AAAGCA------ACA---------AGT------ACAGCC---------ATAATGATGCAGAAAAGCAACTTTAAGGGCCAAAAAAGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAGGGGGAGGCCAGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAACTTCGGGTTCGGAGAGGGGATAACC---CCCTCCCCGAAGCAGGAGCAG---AAAGGC------GAGGAACAG------GCTCCTCCCTTAGTTTCCCTCAAATCACTCTTTGGCAGCGACCCT!!TAGTCGCAAT!AA +>Ref.C.BR.92.BR025_d.U52953 +ATGGGTGCGAGAGCGTCAATATTAAGAGGCGGAAAATTAGATGCTTGGGAAAGAATTAAGTTAAAGCCAGGGGGAAAGAAACACTATATGATGAAACACCTAGTCTGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTGACCCTGGCCTTTTAGAGACA---TCCGAAGGCTGTAAACAAATAATGAAACAGCTACAACCA---GCTCTTCAGACAGGAACAAAGGAACTTATATCATTACATAATACGGTTGCAACTCTCTATTGTGTACAT---GAAAAGATAGATGTACGAGACACCAAGGAAGCCTTAGACAAAATAAAGGAAGAA---CAAAACAAAAGTCAG---------CAAAAAACACAGCAGGCA---GAAGCGGCTGACAAAGGA---------------------------AAGGTCAGTCAAAATTATCCTATAGTACAGAATCTCCAA---GGGCAAATGGTACACCAGCCCATATCAGCTAGAACTTTGAATGCGTGGGTAAAGGTAGTAGAGGAGAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGTTAAATACAGTGGGGGGACACCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAGGCTGCAGAATGGGATAGATTACATCCAGTGCATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACCAGTACCCTTCAGGAACAAATAACATGGATGACAAATAAC---------CCACCTGTCCCAGTAGGAGACATCTATAAAAGATGGATAATTCTGGGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAACTCTAAGAGCAGAGCAAGCTACCCAAGATGTAAAAAATTGGATGACAGATACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCACAAAGCAAGAGTGTTGGCTGAGGCAATGAGC------AAAGTA------AAC---------AAT------ACAAAC---------ATAATGATGCAAAGAAGCAATTGTAAAGGCCCTAAAAGAACTATTAAATGCTTCAACTGTGGCAAGGAAGGGCACTTAGCCAGAAATTGCAGGGCTCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAAGAAGGACACCAAGTGAAAGACTGTACTGAGAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAGGGGGAGGCCAGGAAATCTTCTTCAGAACAGAACA------------------------------GAGCCAACAGCCCCACCAGAA---------------------------------GAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCGGAAGCAGGAGACG---ATAGAC------AAGGAACTG------------CCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCAACATAA--- +>Ref.G.KE.93.HH8793_12_1.AF061641 +ATGGGTGCGAGAGCSTCASTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGSCTGACGCCAGGGGGAAAGAAAAAATACAGACTGAAACATCTAGTATGGGCAAGCAGAGAGATGGAGAGATTTGCACTTAACCCTGGCCTTTTAGAAACA---GCAGAAGGTTGTCAACAAATAATGAGCCAGTTGCAACCA---GCTATCCAMACAGGAACAGAGGAGATTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTACATCCC---AAGATAGAGGTAAAGGACACCAAAGAAGCTCTAGAGGAAGTAGAAAAGATA---CAAAAGAAAAGTCAG---------CAAAAAATACAGCAGGCA------GCAAGGGATGAAGGAAACAGCAGC------------------CAAGTCAGCCAAAATTATCCTATAGTGCAGAACGCACAA---GGACAGATGGTACACCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAAGATACTATCAATGAGGAAGCTGCAGAGTGGGACAGAATACATCCACCACAGGCAGGGCCTATTCCACCAGGCCAAATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACCACTAGTAACCTGCAGGAACAAATAAGATGGATGACCAGCAAC---------CCACCTATCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGACAGGTTCTTTAAAACTTTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATCTTAAGAGCATTAGGACCCGGAGCTACACTAGAAGAAATGATGACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGAGTGTTAGCTGAGGCAATGAGC------CAGGCA------ACA---------GGT------GCAGCAGCA---GCCATAATGATGCAGAAAAGCAACTTTAAGGGCCCGAAAAGAAATATCAAGTGTTTCAATTGTGGCAAGGAAGGACACTTAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGCTGGAAA---TGTGGAAAGGAGGGACATCAAATGAAAGACTGCACGGAAAGACAGGCTAATTTT!TAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTTCTTCAGAACAGGCCA------------------------------GAGCCAACAGCCCCACCCGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAAATAGCC---CCCTCCCCGAAGCCAGAGCCG---AAGGAA------AAGGAGATA---------CATCCCTTAGCTTCCCTCAAATCACTCTTTGGCAGCGACCCC!TAGTCACAGTA!!A +>Ref.A2.CD.97.97CDKTB48.AF286238 +ATGGGTGCGAGAGCGTCAGTATTGAGCGGCGGAAAATTAGAAGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTCTCAATCAACCCCAGCCTTTTAGAAACA---GAAACAGGATGTAGACGAATATTTGGGCAATTACAACCA---GCTCTCGAGACAGGAACAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTACTTTGTTCAT---CAAAAGATAGAGGTAAAAGACACCAAGGAAGCTCTAGATAAAATAGAGGAAGAA---CAAAACAAATGCAAG---------CAGAAGACACAGCAGGCA------GCAGCTGACACAGGAAGCAGCAGCAGTCAAAATTACAGAGGTAGCAGCAGTCAAAATTACCCTATAGTGCAAAATGCACAA---GGGCAAATGGTACACCAGGCCGTGTCACCTAGGACTTTGAATGCATGGGTCAAAGTAGTTGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGTTACATCCAGTACAGGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCGGGAGCTACTAGTAACCTTCAGGAACAAATAGGATGGATGACCAGCAAC---------CCACCTATTCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGACACCTTGCTGGTCCAAAATGCAAACCCAGATTGTAAATCCATCTTGAGGGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTAGCTGAAGCAATGAGC------CAAGTA------CAA---------AAT------ACAAAC---------ATAATGATACAGAGAGGCAATTTTAAGGGTCAAAAAAGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAA---TGTGGGAAGGAAGGACATCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAAGGGAGGCCAGGGAATTTTCCTCAGAGCAGGACA------------------------------GAGCCAACAGCCCCACCAATG---------------------------------GAG---------------GAAGAGATAACC---TCCTCGCTGAAGCAGGAGAAC---AGGGAG------CCGTCCACC------------CCTGCAATTTCCCTCAAATCACTCTTTGGCAACGACCTCTTGTCACAGTGA--- +>Ref.G.BE.96.DRCBL.AF084936 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAGATATAGAATGAAACATTTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTTTTAGAAACA---GCAGAAGGTTGTCAAAAAATAATGGCACAGTTGCAACCA---GCTCTCCAAACAGGAACAGAGGAGATTAAATCACTATTTAATACAGTAGCAACCCTCTATTGTGTACAT---CAAAAGATAGAGGTAAGAGACACCAAAGAGGCTCTAGAGGAAGTGGAAAAGATA---CAAAAGAAGAGTCAG---------CAAAAAGAAAACAGCAGC------AGC---------------------------------------CAAGTCAGTCAAAATTACCCTATAGTGCAGAATGCACAA---GGGCAAATGGTACACCAGGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAATACAGTGGGGGGGCATCAAGCAGCTATGCAAATGTTAAAGGAGACTATCAATGATGAAGCTGCAGAATGGGACAGGCTACATCCACAGCAGGCAGGGCCTATTGCACCAGGCCAGATAAGGGACCCAACGGGAAGTGATATAGCAGGAGCTACTAGTACCCTGCAGGAACAGATAAGATGGATGACCAGCAAC---------CCACCTGTCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGGTTAAATAAAATAGTAAGAATGTACAGCCCTGTCAGCATTTTGGACATAAGACAGGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGATTCTTTAAAACCCTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAAGCTGGATGACAGACACCTTGTTGATCCAAAATGCAAACCCAGATTGTAAGATCATCTTAAAAGGATTAGGACAAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATGAGC------CAGGCA------TCA---------GGT------GCAGCAGCA---GCCATAATGATGCAGAAAAGCAATTTCAAGGGCCCAAGAAGAACAATTAAATGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACATCAAATGAAAGAATGCACAGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGGCCA------------------------------GAGCCAACAGCCCCACCCGCA---------------------------------GAGAACTTCGGGTTCGGGGAGGAGATAGCC---CCCTCCCCGAAGCAGGAGCAG---AAGGAA------AAGGAACTA---------TATCCTCTATCTTCCCTCAAATCACTCTTTGGCAAC!GACCAATAGTCAAAGTA!!A +>Ref.K.CD.97.97ZR_EQTB11.AJ249235 +ATGGGTGCGAGAGCTTCAGTATTAAGCGGGGGAAAATTAGACAAATGGGAAAAAATTCAGTTACGGCCAGGGGGAAAGAAAAAATACAGGCTAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTAACCTTTTAGAGACA---GTAGAAGGCTGTCGGCAAATAATAAGACAACTACAACCA---TCCCTTCAAACAGGCTCGGAAGAGCTTAGATCACTATTTAATACAGTAGCAACCCTCTATTGGGTGCAT---CAAAGTATACAGGTAAGGGACACCAAGGAAGCCTTAGACAAACTAGAGGAAGAA---CAAAACAGAACTCAG---------CAAAAGACACAGCAAGGA------AAAGCTGACAAAGGG------------------------------GTTAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGGCAAATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTTAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACTCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATGAGGAAGCTGCAGAATGGGACAGGATGCACCCAGTGCAAGCAGGGCCTATCCCACCAGGCCAAATAAGAGAACCTAGGGGGAGTGATATAGCAGGAACTACTAGCACTCTTCAGGAACAAATAACATGGATGACAAGCAAC---------CCACCTATCCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGGTTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAGAGTTCTAAGAGCTGAACAAGCCACACAGGAAGTAAAAAATTGGATGACAGAAACCCTGTTGGTCCAAAACGCAAACCCAGATTGTAGGACCATTTTAAAGGCGTTGGGATCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGGCCTGGCCATAAAGCAAGGGTTTTGGCTGAGGCAATGAGC------CAGGTA------ACA---------AAT------TCAGCC---------GTAATGATGCAGAGAGGCAACTTTAAGGGTCAAAGAAGAATTATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGAAATTGTAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGGAAAGAAGGACATCAGATGAAAGACTGTTCTGAGAGACAGGCTAATTTTTTAGGGAAGTTCTGGCCTCTCAACAAAGAGAGGCCAGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTTGGGTTCGGGGAGAAGATAACC---CCCTCTCTGAGACAGGAAATG---AAAGAT------CAGGAACAG------GGTCCTCCTTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCGTTGTCACAGTAA--- +>Ref.D.TZ.01.A280.AY253311 +------GCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATGCATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAACTAAAACATATAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---TCCGAAGGCTGTAAACAAATC!TA---------CAACCA---GCTATTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTGCAT---AGAAAGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAAAAATTAGAGGAAGAG---CAAACCAAAAGTAAG---------AAAAAGGCACAGCAAGCA------ACAGCTGACACAGGAAGCAGCAGC------------------CAGGTCAGCCAAAATTATCCTATAGTGCAAAACCTACAG---GGGCAAATGGTACACCAGGCCATATCACCTAGAACCTTGAACGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACAATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATTGCACCAGGACAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAATAAT---------CCACCTGTCCCAGTAGGAGAAATATATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAGACAAGGACCAAAGGAGCCCTTTAGGGACTATGTAGATCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGATGTAAAAAATTGGATGACTGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAAACTATCTTAAAAGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCAGTCATAAGGCAAGAGTTCTAGCTGAGGCAATGAGC------CAAGCA------ACA---------AAT------GTAAATGCT---GCCATAATGATGCAGAGAGGTAATTTTAAGGGCCCAAGGAAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGACACATAGCAAAAAATTGCAGGGCCCCAAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGATTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAAAGGAAGGCCAGGGAACTTCCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGATCTTCGGGTTTGGGGAGGAGATAAAA---CCCTCTCAGAAACAGGAGCAG---AAAGACAAGGACAAGGAACTG---------TATCCTTCAGCTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAA--- +>Ref.F2.CM.02.02CM_0016BBY.AY371158 +------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGACTGGGAGAAAATTCGGTTAAGGCCGGGAGGGAAGAAAAAATATAGGCTAAAACATATAGTATGGGCAAGCAAGGAGCTAGAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---ACAGAAGGCTGTAAACAAATAATAGGACAACTACAA---TCATCCCTTCAGACAGGATCAGAAGAGATTAAATCATTATATAACACAGTAGCAGTCCTCTATTATGTACAT---CAAAAGATACAAATAAGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGACAAATATCAG---------CAAAAAACACAACCAGCA------GCGGCTGATAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGGCAAATGGTACATCAGGCTATATCACCTAGAACTCTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTCATACCCATGTTTTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTAGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCAGGCAGGACCTATCCCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCACTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAATTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------GCT------ACATCC---------GTACTGATGCAGAAAAGCAACTTTAAGGGCCAAAAAAGAATTGTCAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAAAATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAAGGGAGGCCTGGGAATTTCATTCAGAGCAGACCA------------------------------GAGCCAACGGCCCCGCCAGCA---------------------------------GAGGGCTTCGGGTTCGGAGAAGAGATAACT---CCCTCCCCGAAGCAGGAGCAG---AAAGAC------AAGGGACTG------TATCCTCCCTTGACTTCCCTCAAATCACTCTTTGGCAACGACCCG!TAGTCACAATA!!A +>Ref.F1.BE.93.VI850.AF077336 +ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGAATGGGAAAAAATTCAGTTAAGGCCGGGGGGAAAGAAAAGATATAAAATGAAACATCTAATATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCTGGCCTTCTAGAAACA---TCAGAAGGCTGTCAAAAAATAATAAGACAGCTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTTAAGTCATTATTTAATACAGTAGCAGTCCTCTATTATGTACAT---CAAAGGGCAGGGGTAACAGACACCAAGGAAGCTTTAGACAAGCTAGAGGAAGAA---CAAAACAAAAGTCAG---------CAAAAGACACAGCAAGCG------GCAGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAGGTGATAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACTCCCACAGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGGCCTGCCCCACCAGGCCAGATGAGGGAACCTAGGGGGAGTGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACGGGCAAC---------CCACCTGTCCCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGATTCTTTAAAGTCCTAAGAGCTGAGCAAGCTTCACAGGACGTAAAGGGTTGGATGACAGACACATTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCATTGGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCCGAGGCAATGAGT------CAAGCA------------------AAT------TCAGCC---------ATAATGATGCAGAAAAGTAATTTTAAGGGCCAAAGAAGAGTTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAGAGAAGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTCCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCAGAGAGGAGATAACC---CCCTCTCCGAAGCAGGAGCAG---AAAGAC------GGGGAACTG------TACCCTCCCTTAGCTTCCCTCAAATCACTCTTTGGCAACGACCCT!TAGTCACAATA!!A +>Ref.B.NL.00.671_00T36.AY423387 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATAGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAGAGAGCTAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACA---TCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCA---GCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTGCAT---GCAAGGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAAAAAATAGAGGAAGAA---CAAAACAAAAGTAAGAAACGGGCACAGCAAGCACAGCAAGCA------GAAGCTGACGCAGGAAAAAACAAC------------------CCGGTCAGCCAGAATTACCCTATAGTGCAGAATCTCCAA---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCCTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCCGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAAT---------CCACCTATCCCAGTAGGAGAAATATATAAGAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAAACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAACTTTAAGAGCTGAGCAAGCCTCACAGGAAGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATTCGAACCCAGATTGTAAAACTATTTTAAAAGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACCGCATGTCAGGGAGTAGGGGGACCCGGCCATAAAGCGAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AGT------GCACCT------GCCATAATGATGCAGAGAGGCAATCATAGAAACCAAAGAAGGACTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAGAAATTGCAGGGCCCCTAGNAAAAAGGGCTGTTGGAAA---TGTGNAAAGNAAGGACACCAAATGAAAGATTGTACTNAGAGACAGGCTANTTTTTTAGGGAAGATTTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCTTCTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAA---------------------------------GAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAGGCAGGAGCCA---ACAGAC------AAGGAACTG---------TATCCTTTAGCTTCCCTCAAATCACTCTTTGGCAGCGACCCA!TAGTCACAATA!!A +>Ref.C.IN.95.95IN21068.AF067155 +ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATAAATGGGAAAAAATTAGGTTAAGGCCAGGGGGAAAGAAACGCTATATGCTAAAACACCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCAGTTAACCCTGGCCTTTTAGAGACA---GCAGAAGGCTGTAAACAAATAATAAAACAGCTACAACCA---GCTCTTCAGACAGGAACAGAGGAACTTAGATCATTATTCAACACAGTAGCAACTCTCTATTGTGTACAT---GCAGGGATAGAAGTACGAGACACCAAAGAAGCCTTAGACAAGATAGAAGAAGAA---CAAAACAAAATTAAG---------CAAAAAACACAGCAGGCA------AAAGAGGATGACGGG---------------------------AAGGTCAGTCAAAATTATCCTATAGTGCAGAATCTCCAA---GGGCAAATGGTACACCAAGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAGTAATAGAGGAAAAGGCTTTTAGCCCAGAGGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGTTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAAGAGGCTGCAGAATGGGATAGATTACATCCAGTACCTGCAGGGCCTATTGCACCAGGCCAACTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACGAATAAC---------CCACCTGTTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTGAGCATTTTGGACATAAGACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAACTTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAATCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGCCACAAAGCAAGAGTGTTGGCTGAGGCAATGAGC------CAA---------ACA---------AAC------AGTGCC---------ATACTGATGCAAAGAAGCAATTTTAAAGGCTCTAAAAGAATTGTTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTCCTCCAGAGTAGACCA------------------------------GAGCCAACAGCTCCACCAGCA---------------------------------GAGAGCTTCAGGTTC---GAGGAGACAACC---CCAGCTCCGAAGCAGGAGCCG---AAAGAC------AGGGAA---------------CCTTTAACTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTCTCAATAA--- +>Ref.B.US.98.1058_11.AY331295 +------------GCGTCAGTATTAAGCGGGGGAAAATTAGATACATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTGGCCTGTTAGAAACA---GCAGAAGGCTGTAGACAATTATTGGGACAGCTACAGCCA---TCCCTTCAAACAGGATCAGAAGAACTTAAATCATTATTTAATACAATAGCAACCCTCTATTGTGTACAT---CAAAGGATAGAGGTAAGAGACACCAAAGAGGCTTTAGACAAGATAGAGGAAGAG---CAAAACAAAAGTAAG---------AAAAAAGCACAGCAAGCAGCAGCTGCAGCTGACACAGGAAACAGCAGC------------------CAGGTCAGCCAAAATTACCCTATAGTGCAGAACCTCCAA---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTGCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAAACCATCAATGAGGAAGCTGCAGAATGGGATAGAATACATCCAGCGCAAGCAGGGCCTATAGCACCAGGCCAGATAAGAGACCCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAACATGGATGACAAATAAT---------CCACCTATCCCAGTAGGAGAAATCTATAAAAAATGGATAATCATGGGATTAAATAAAATAGTAAGGATGTATAGTCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGGGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAACGCGAACCCAGATTGTAAGACTATATTAAAAGCATTAGGACCAGCAGCTACACTAGAGGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATGAGC------CAAGTA------ACA---------AAT------TCAGGT------GCCATAATGATGCAGAAAGGCAATTTTAGGAACCAG------GTTGTTAGGTGTTTCAATTGTGGCAAAGTAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAAA---TGTGGAAAAGAAGGACACCAAATGAAAGATTGTGATCAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCCACAAAGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCAGGTTTGGGGAGGAGACAACAACTCCCTCTCAGAAGCAGGAGCCA---CAAGAA------------------------TATCCTTTAGCTTCCCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAA--- +>Ref.J.CD.97.J_97DC_KTB147.EF614151 +------------------------------------------GCATGGGAGAAAATTTGGCTGAGGCGACGGGGAGAGAAAAAATACAGGCGAAAACATATAGTATGGGCAAGCAGGGAGCTGGACAGATATGCACTTAACCCTGGCCTTCTA!!TAGT!GAGCAGAAGGCGGTGAACAGATACTAGTACAGATCCAACCA!GATCTTTA!!AACAGGAGCAGAGGAGATAAAATCATTATTTAACACAGAAGCAACCCTCTATTGTGTACAT!!T!AGAGGATAGACATAAGAGACACCAAGGAGGCTTTAGACAAGATAGAGGAA!CTTTA!!AAACAAAAGCAAG---------GAGAAAGCTAAGAAAGAA------GCTGTCAAAAAATACAACAGT---------------------CAGGTGAGTCACAATTATCCTATATTGCAAAATATG!!T!AAGGGGAACTAGTACACCAGGCCCTATCACCTAGAACATTAAATGCATGGGTAAAGGTGATAGAAGAGAAAGGTTTCAACCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACTCCACAAGATTTAAATACCATGCTAAACACGGTGGGGGGACATCAAGCAGCGATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGCTCCATCCAGTACATGCAGGACCTGTTGCACCAGGTCAGATGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTACTAGTAACCTTCAGGAACAAATAGCATGGATAACAGGCAACGGTGGCAACCAACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATTTTAGGATTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGGCAAGGACCAAAAGAACCTTTTAGAGACTATGTGGATAGGTTCTTTAAAACTCTAAGAGCCGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGATACCTTGTTGGTCCAAAATGCGAATCCAGATTGTAAGACCATTCTAAGAGCATTAGGAGCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGAGAGTATCCAGTCATAGAGCAAGAGTTTTTGGTGAGGCAATAAGC------CAAGTA------AAC---------AAT------ACAAAC---------ATAATAATGCAAAGAGGTAACTTTAGGGGCCAGAAGAGAAGTGTTAAATGTTTCAACTGTGGTAAAGAGGGACACATAGCAAAAAATTGCAGGGCCCCTAGAAAAAAGGGCTGT!TGAAA!!GTGTGGAAAGGAAGGACACCAAATAAAAAACTGCACTGAGAGACAGGCCAATTTTTTAGGGAAAGTTTGGCCTTCCAGCAAGGGGAGGCCAGGGAACTTTCTCCAGAGCAGGCCA------------------------------GAACCAACAGCCCCACCAGCA---------------------------------GAAAGCTTCGGGTTCGGGGAGAAGATAACT---CCCTCCCAGAAACAGGAACCG---AGG---------AAGGAACTA---------TATCCTTCAGCTTCCCTCAAATCACTCTTTGGCAGCGACCCCTCGTCACAGTAA--- +>Ref.J.CM.04.04CMU11421.GU237072 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATACTTGGGAGAAAATTCGGTTGAGGCCAGGGGGGAAGAAACGTTATAGGCTAAAACATTTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGRCCTTCTAGAAACA---TCAAAAGGCTGTCAACAAATATTAGTACAGCTCCAACCA---TCTTATCAAACAGGGACAGAAGAAATTAAGTCATTATATAACACAGTAGCAACCCTCTATTGCGTACAT---GAGGRSATAGAGGTAAAAGACACCAAGGAARCTTTAGACAAGATAGAGGAACTA---CAAAAGAAGAACAAG---------CAACAGGCACAGAAAGCA------GAARCTGACAAAAGRRACARCAGT------------------CAAGTCAGTCAAAATTATCCTATAGTGCAGAACATGCAA---GGGCAACCAGTACAYCARGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTGRTAGAAGARAAGGCTTTYAGCCCAGAAGTAATACCCATGTTTTCAGCYTTATCAGAAGGAGCCACCCCRCAAGATTTAAATACCATGCTAAATACAGTRGGGGGACACCARGCAGCTATGCAAATGTTAAAAGATACTATCAATGAGGAAGCTGCAGAATGGGATAGGKTACATCCAGTACATGCAGGGCCTCCRGCACCAGGCCAGGCGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTCCAGGAACAAATAGCATGGATGACAGGCAAC---------CCACCTATCCCAGTAGGGGAAATTTATAAAAGRTGGATAATTCTGGGATTAAATAAAATAGTRAGAATGTATAGCCCTGTCAGCATTTTGGATATAAGACAAGGACCAAAAGARCCTTTTAGAGAYTATGTAGATCGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGATACCTTGTTGATCCAAAATGCAAATCCAGATTGCAGAACCATYTTAAAAGCATTAGGACCAGGAGCTACACTAGARGAAATGATGACAGCATGYCAGGGAGTGGGAGGACCTGGTCATAAAGCAAGAGTTTTGGCWGAAGCAATGAGC------CAAATG------ACC---------AAT------ACAGCA------AACATAATGATGCAAARGGGTAAYTTTAAGGGCCARAAAAGAATGATTAAGTGTTTCAATTGTGGWAAACCAGGACACCTAGCMAGAAAYTGCAGAGCCCCTAGRAARAAGGGCTGTTGGAAA---TGTGGACAGGAAGGACAYCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAARATCTGGCCTTCCAACAARGGGAGGCCAGGGAACTTTCTYCAGAGCAGRCCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAAGAG---ACC---YCYYCCCCGAAACAAGAAGCG---------------AAGGAACTG---------TATCCTCTAACTTCCCTCAAATCACTCTTTGGCARCGACCCCTYGTCACAATAA--- +>Ref.H.GB.00.00GBAC4001.FJ711703 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTCAACCCCGACCTTTTAGAAACA---GCAGATGGCTGTCTAAAAATAYTAGGACAGATACAGCCA---GCTCTTCAGACAGGAACAGAAGAAATTAAATCGTTATTTAATCTAGTAGCAGTCCTCTATTGTGTACAT---CAGAAAATAGAGGTACAAGATACCAGTGAAGCTTTAAATAAGGTAAAGGAGATA---CAGAACAAGAACCAG---------CAAACAACACAGCAGGCA------ACAGCTRGTAAAGAGAAGGACAGC------------------AAGATCAGTCAAAATTATCCTATAGTACAGAATGCCCAA---GGGCAAATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGARGGAGCMACCCCACAAGACYTAAATACCATGTTAAACTCAGTGGGGGGACATCAGGCAGCCATGCAAATRTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGATAGGACACATCCAGTGCATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTACTAGYAACCTTCAGGAACAAATAGCATGGATGACARGYAAT---------CCCCCTRTCCCAGTGGGRGAKATCTATAAAAGATGGATAATCWTGGGATTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGAYTATGTAGACAGGTTYTTTAAAACTTTAAGAGCTGAGCAAGCCACACAGGACGTGAAGAATTGGATGACAGACACCTTGTTGGTCCAAAATGCAAATCCAGATTGCAAGACTATTTTAAAAGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGT------CAAATG------ACA---------AAT------ATGAATACA---GCCATAATGGTGCAGAAAGGCAACTTTAAGGGCCAAAGAAGAACTGTTAAATGTTTCAACTGTGGTAAAGAAGGACACATAGCAAGAAACTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGGAGGGAAGGACATCAGATGAAAGACTGCACAGAGAGACAGGCGAATTTTTTAGGGAAAATCTGGCCTTCCAGCAAAGGGAGGCCAGGGAACTTTCTCCAGAGCAGGCCA------------------------------GAACCAACAGCCCCACCAGCA---------------------------------GAATGCTTCGGGTTCGGGGAGGAGATGACA---CCCCCTCCGAAGCAGGAGATG---AAGGAA------AAGGAA------------CCTCCCTTAACTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTCACAGTAA--- +>Ref.G.NG.92.92NG083.U88826 +GTGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATTCTTGGGAAAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAGTATAAACTAAAACATATAGTATGGGCAAGCAGGGAACTGGGGAGATTTGCACTTAACCGTGACCTTTTAGAAACA---GCAGAAGGTTGTGTGCAAATAATGAAACAGTTGCAACCA!GCTCTCTA!!GACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAACCCTCTACTGTGTACAT---CAAAAGATAGAGGTAAAAGACACCAAAGAAGCTCCAGAGGAAGTGGAAAAAATA---CAAAAGAACAGTCAG---------CAAGAAATACAGCAGGCA------GCAAAGAATGAAGGAAACAGTAAC------------------CCAGTCAGCCAAAATTATCCTATAGTGCAGAATGCACAA---GGGCAAATGATACATCAGGCCATATCACCTAGGACTTTGAATGCGTGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAGGGAGCCACCCCACAAGATTTAAATACCATGCTAAATACAGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATCAATGATGAAGCTGCAGAGTGGGACAGGATACATCCACAGCAGGCAGGGCCTATTCCACCAGGCCAAATAAGAGAGCCTAGTGGAAGTGATATAGCAGGAACTACTAGTACCCTGCAGGAACAAATAAGATGGATGACCAGCAAC---------CCACCTATCCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAACTTTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGTTGGATGACAGACACCTTGTTGGTTCAAAATGCGAACCCAGATTGTAAAACCATCTTAAGAGCATTAGGACCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATGAGC------CAGGCA------TCA---------GGT------GCAGCAGCAGCAGCCATAATGATGCAGAAAAGCAATTTTAAGGGCCCGAGAAGAATTATTAAGTGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACATCAAATGAAAGAATGCACGGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGAAACTTTCTCCAGAACAGGACA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGATTCGGAGAGGAGATAGCC---CCCTCCCCGAAGCAGGAGCCA---AAGGAG------AAGGAGCTA---------TATCCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCC!TAGTCACAGTA!!A +>Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACA---TCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCA---TCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCAT---CAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAG---CAAAACAAAAGTAAG---------AAAAAAGCACAGCAAGCA------GCAGCTGACACAGGACACAGCAAT------------------CAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAG---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAAT---------CCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGC------CAAGTA------ACA---------AAT------TCAGCT------ACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGAA---------------------------------GAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCG---ATAGAC------AAGGAACTG---------TATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAA--- +>Ref.B.TH.90.BK132.AY173951 +ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATAGATGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTATTGGAAACA---TCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCA---AGCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGTGTACAT---CAAAAGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAGAAGATAGAGGAAGAA---CAAAACAAAAGTAAG---------AAAAAGGCACAGCAAGCA------GCAGCTAACACAGAAAACAGCAGC------------------CAGGTTAGCCAAAATTACCCTATAGTGCAAAATATGCAG---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACACATAAT---------CCACCTATCCCAGTGGGAGAAATTTACAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGGATGTATAGCCCTACCAGCATTTTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAGACTCTAAGAGCCGAGCAAGCCTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGTCCCGGCCATAAGGCAAGAGTTTTGGCGGAAGCAATGAGC------CAAGTG------ACA---------AAT------TCAGCT------ACCATAATGATGCAGAAAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCCGAAATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAGA---TGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAAAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCGACAGCCCCACCAGCA---------------------------------GAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGACA---ATAGAC------AAGGAACTA---------TATCCTTTAACTGCCCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAA--- diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -99,7 +99,7 @@ optimization.max_number_f_eval = 10000 # Precision to reach: -optimization.tolerance = 1 //0.000001 +optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/M0/ML.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/M0/ML.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/M0/ML.bpp 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/M0/ML.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,155 @@ +#Example data set adapted from PAML +# +#logL = 65442.80353609310986939818 + +# Global variables: +DATA = lysozymeLarge + +# Sequences: + +# The alphabet to use: +# DNA, RNA or Protein... +alphabet=Codon(letter=DNA, type=Standard) + +# The sequence file to use (sequences must be aligned!) +input.sequence.file=../../../Data/$(DATA).fasta + +# The alignment format: +input.sequence.format=Fasta + +#Sites to use: +# all, nogap or complete (=only resolved chars) +input.sequence.sites_to_use = all +# Specify a maximum amount of gaps: may be an absolute number or a percentage. +input.sequence.max_gap_allowed = 50% + +input.sequence.remove_stop_codons = yes + +# ---------------------------------------------------------------------------------------- +# Input tree file +# ---------------------------------------------------------------------------------------- + +# user or random +init.tree = user + +input.tree.file = ../../../Data/$(DATA).dnd +input.tree.format = Newick + +init.brlen.method = Input + +# ---------------------------------------------------------------------------------------- +# Model specification +# ---------------------------------------------------------------------------------------- +# See the manual for a description of the syntax and available options. +# +model = YN98(kappa=1, omega=1.0, frequencies=F0) +nonhomogeneous=no + +rate_distribution = Uniform //Gamma(n=4, alpha=0.358) + +# Likelihood recursion option: +# - simple: derivatives takes more time to compute, but likelihood computation is faster. +# For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. +# - double: Uses more memory and need more time to compute likelihood, due to the double recursion. +# Analytical derivatives are however faster to compute. +# This option has no effect in the following cases: +# - Topology estimation: this requires a double recursive algorithm, +# - Optimization with a molecular clock: a simple recursion with data compression is used in this case, +# due to the impossibility of computing analytical derivatives. +likelihood.recursion = simple + +# Site compression for the simple recursion: +# - simple: identical sites are not computed twice +# - recursive: look for site patterns to save computation time during optimization, but +# requires extra time for building the patterns. +# This is usually the best option, particularly for nucleotide data sets. +likelihood.recursion_simple.compression = recursive + +# ---------------------------------------------------------------------------------------- +# Optimization +# ---------------------------------------------------------------------------------------- + +# Should we reestimate likelihood parameters? Tree topology will not be optimized. +# (recommanded) +optimization = FullD(derivatives=Newton) + +# Tell if the parameter should be transformed in order to remove constraints. +# This can improves the optimization, but might be a bit slower. +optimization.reparametrization = no + +# Final optimization step, may be useful if numerical derivatives are used: +# powell or simplex or none. +optimization.final = none + +# Set the quantity of output to the screen: +optimization.verbose = 3 + +# Parameters to ignore (for instance equilibrium frequencies) +optimization.ignore_parameter = + +# Maximum number of likelihood evaluations: +optimization.max_number_f_eval = 10000 + +# Precision to reach: +optimization.tolerance = 0.000001 + +# idem for error or warning messages: +optimization.message_handler = $(DATA).messages + +# A file where to dump optimization steps (a file path or std for standard output) +optimization.profiler = $(DATA).profile + +# Shall we optimize tree topology as well? +optimization.topology = no + +# Algorithm to use for topology estimation: only NNI for now +optimization.topology.algorithm = NNI + +# NNI method: fast, better or phyml +# You should use the phyml option, since it is really more efficient! +optimization.topology.algorithm_nni.method = phyml + +# Number of phyml topology movement steps before reoptimizing parameters: +optimization.topology.nstep = 4 + +# Shall we estimate parameters before looking for topology movements? +optimization.topology.numfirst = no + +# Tolerances: These numbers should not be too low, in order to save computation +# time and also for a better topology estimation. +# The optimization.tolerance parameter will be used for the final optimization +# of numerical parameters. +# +# Tolerance for the prior-topology estimation +optimization.topology.tolerance.before = 100 + +# Tolerance for the during-topology estimation +optimization.topology.tolerance.during = 100 + +# Shall we first scale the tree before optimizing parameters? [deprecated] +optimization.scale_first = no + + + + +# Should we write the resulting tree? none or file name. +output.tree.file = $(DATA).ML.dnd +output.tree.format = Newick + +# Alignment information log file (site specific rates, etc): +output.infos = $(DATA).infos + +# Write numerical parameter estimated values: +output.estimates = $(DATA).params.txt + +# ---------------------------------------------------------------------------------------- +# Bootstrap +# ---------------------------------------------------------------------------------------- + +bootstrap.number = 0 +# Tell if numerical parameters should be kept to their initial value when bootstrapping: +bootstrap.approximate = no +# Set this to yes for detailed output when bootstrapping. +bootstrap.verbose = no +bootstrap.output.file = $(DATA).ML_bstrees.dnd + diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/M1/ML.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/M1/ML.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/M1/ML.bpp 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/M1/ML.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,155 @@ +#Example data set adapted from PAML +# +#Initial log likelihood.................: -1069.68587126864 + +# Global variables: +DATA = lysozymeLarge + +# Sequences: + +# The alphabet to use: +# DNA, RNA or Protein... +alphabet=Codon(letter=DNA, type=Standard) + +# The sequence file to use (sequences must be aligned!) +input.sequence.file=../../../Data/$(DATA).fasta + +# The alignment format: +input.sequence.format=Fasta + +#Sites to use: +# all, nogap or complete (=only resolved chars) +input.sequence.sites_to_use = all +# Specify a maximum amount of gaps: may be an absolute number or a percentage. +input.sequence.max_gap_allowed = 50% + +input.sequence.remove_stop_codons = yes + +# ---------------------------------------------------------------------------------------- +# Input tree file +# ---------------------------------------------------------------------------------------- + +# user or random +init.tree = user + +input.tree.file = ../../../Data/$(DATA).dnd +input.tree.format = Newick + +init.brlen.method = Input + +# ---------------------------------------------------------------------------------------- +# Model specification +# ---------------------------------------------------------------------------------------- +# See the manual for a description of the syntax and available options. +# +model = YNGKP_M1(kappa=1, omega=1.0, frequencies=F3X4, p0=1.0, initFreqs=observed) +nonhomogeneous=no + +rate_distribution = Uniform //Gamma(n=4, alpha=0.358) + +# Likelihood recursion option: +# - simple: derivatives takes more time to compute, but likelihood computation is faster. +# For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. +# - double: Uses more memory and need more time to compute likelihood, due to the double recursion. +# Analytical derivatives are however faster to compute. +# This option has no effect in the following cases: +# - Topology estimation: this requires a double recursive algorithm, +# - Optimization with a molecular clock: a simple recursion with data compression is used in this case, +# due to the impossibility of computing analytical derivatives. +likelihood.recursion = simple + +# Site compression for the simple recursion: +# - simple: identical sites are not computed twice +# - recursive: look for site patterns to save computation time during optimization, but +# requires extra time for building the patterns. +# This is usually the best option, particularly for nucleotide data sets. +likelihood.recursion_simple.compression = recursive + +# ---------------------------------------------------------------------------------------- +# Optimization +# ---------------------------------------------------------------------------------------- + +# Should we reestimate likelihood parameters? Tree topology will not be optimized. +# (recommanded) +optimization = D-Brent(derivatives=Newton, nstep=10) + +# Tell if the parameter should be transformed in order to remove constraints. +# This can improves the optimization, but might be a bit slower. +optimization.reparametrization = no + +# Final optimization step, may be useful if numerical derivatives are used: +# powell or simplex or none. +optimization.final = none + +# Set the quantity of output to the screen: +optimization.verbose = 3 + +# Parameters to ignore (for instance equilibrium frequencies) +optimization.ignore_parameter = YNGKP_M1.freq* + +# Maximum number of likelihood evaluations: +optimization.max_number_f_eval = 10000 + +# Precision to reach: +optimization.tolerance = 0.000001 + +# idem for error or warning messages: +optimization.message_handler = $(DATA).messages + +# A file where to dump optimization steps (a file path or std for standard output) +optimization.profiler = $(DATA).profile + +# Shall we optimize tree topology as well? +optimization.topology = no + +# Algorithm to use for topology estimation: only NNI for now +optimization.topology.algorithm = NNI + +# NNI method: fast, better or phyml +# You should use the phyml option, since it is really more efficient! +optimization.topology.algorithm_nni.method = phyml + +# Number of phyml topology movement steps before reoptimizing parameters: +optimization.topology.nstep = 4 + +# Shall we estimate parameters before looking for topology movements? +optimization.topology.numfirst = no + +# Tolerances: These numbers should not be too low, in order to save computation +# time and also for a better topology estimation. +# The optimization.tolerance parameter will be used for the final optimization +# of numerical parameters. +# +# Tolerance for the prior-topology estimation +optimization.topology.tolerance.before = 100 + +# Tolerance for the during-topology estimation +optimization.topology.tolerance.during = 100 + +# Shall we first scale the tree before optimizing parameters? [deprecated] +optimization.scale_first = no + + + + +# Should we write the resulting tree? none or file name. +output.tree.file = $(DATA).ML.dnd +output.tree.format = Newick + +# Alignment information log file (site specific rates, etc): +output.infos = $(DATA).infos + +# Write numerical parameter estimated values: +output.estimates = $(DATA).params.txt + +# ---------------------------------------------------------------------------------------- +# Bootstrap +# ---------------------------------------------------------------------------------------- + +bootstrap.number = 0 +# Tell if numerical parameters should be kept to their initial value when bootstrapping: +bootstrap.approximate = no +# Set this to yes for detailed output when bootstrapping. +bootstrap.verbose = no +bootstrap.output.file = $(DATA).ML_bstrees.dnd + diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/M2/ML.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/M2/ML.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Codons/M2/ML.bpp 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Codons/M2/ML.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,155 @@ +#Example data set adapted from PAML +# +#Initial log likelihood.................: -1068.04967173634 + +# Global variables: +DATA = lysozymeLarge + +# Sequences: + +# The alphabet to use: +# DNA, RNA or Protein... +alphabet=Codon(letter=DNA, type=Standard) + +# The sequence file to use (sequences must be aligned!) +input.sequence.file=../../../Data/$(DATA).fasta + +# The alignment format: +input.sequence.format=Fasta + +#Sites to use: +# all, nogap or complete (=only resolved chars) +input.sequence.sites_to_use = all +# Specify a maximum amount of gaps: may be an absolute number or a percentage. +input.sequence.max_gap_allowed = 50% + +input.sequence.remove_stop_codons = yes + +# ---------------------------------------------------------------------------------------- +# Input tree file +# ---------------------------------------------------------------------------------------- + +# user or random +init.tree = user + +input.tree.file = ../../../Data/$(DATA).dnd +input.tree.format = Newick + +init.brlen.method = Input + +# ---------------------------------------------------------------------------------------- +# Model specification +# ---------------------------------------------------------------------------------------- +# See the manual for a description of the syntax and available options. +# +model = YNGKP_M2(kappa=1, omega0=0.5, omega2=2.0, frequencies=F3X4, theta1=0.33333, theta2=0.5, initFreqs=observed) +nonhomogeneous=no + +rate_distribution = Uniform //Gamma(n=4, alpha=0.358) + +# Likelihood recursion option: +# - simple: derivatives takes more time to compute, but likelihood computation is faster. +# For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. +# - double: Uses more memory and need more time to compute likelihood, due to the double recursion. +# Analytical derivatives are however faster to compute. +# This option has no effect in the following cases: +# - Topology estimation: this requires a double recursive algorithm, +# - Optimization with a molecular clock: a simple recursion with data compression is used in this case, +# due to the impossibility of computing analytical derivatives. +likelihood.recursion = simple + +# Site compression for the simple recursion: +# - simple: identical sites are not computed twice +# - recursive: look for site patterns to save computation time during optimization, but +# requires extra time for building the patterns. +# This is usually the best option, particularly for nucleotide data sets. +likelihood.recursion_simple.compression = recursive + +# ---------------------------------------------------------------------------------------- +# Optimization +# ---------------------------------------------------------------------------------------- + +# Should we reestimate likelihood parameters? Tree topology will not be optimized. +# (recommanded) +optimization = D-Brent(derivatives=Newton, nstep=10) + +# Tell if the parameter should be transformed in order to remove constraints. +# This can improves the optimization, but might be a bit slower. +optimization.reparametrization = no + +# Final optimization step, may be useful if numerical derivatives are used: +# powell or simplex or none. +optimization.final = none + +# Set the quantity of output to the screen: +optimization.verbose = 3 + +# Parameters to ignore (for instance equilibrium frequencies) +optimization.ignore_parameter = YNGKP_M1.freq* + +# Maximum number of likelihood evaluations: +optimization.max_number_f_eval = 10000 + +# Precision to reach: +optimization.tolerance = 0.000001 + +# idem for error or warning messages: +optimization.message_handler = $(DATA).messages + +# A file where to dump optimization steps (a file path or std for standard output) +optimization.profiler = $(DATA).profile + +# Shall we optimize tree topology as well? +optimization.topology = no + +# Algorithm to use for topology estimation: only NNI for now +optimization.topology.algorithm = NNI + +# NNI method: fast, better or phyml +# You should use the phyml option, since it is really more efficient! +optimization.topology.algorithm_nni.method = phyml + +# Number of phyml topology movement steps before reoptimizing parameters: +optimization.topology.nstep = 4 + +# Shall we estimate parameters before looking for topology movements? +optimization.topology.numfirst = no + +# Tolerances: These numbers should not be too low, in order to save computation +# time and also for a better topology estimation. +# The optimization.tolerance parameter will be used for the final optimization +# of numerical parameters. +# +# Tolerance for the prior-topology estimation +optimization.topology.tolerance.before = 100 + +# Tolerance for the during-topology estimation +optimization.topology.tolerance.during = 100 + +# Shall we first scale the tree before optimizing parameters? [deprecated] +optimization.scale_first = no + + + + +# Should we write the resulting tree? none or file name. +output.tree.file = $(DATA).ML.dnd +output.tree.format = Newick + +# Alignment information log file (site specific rates, etc): +output.infos = $(DATA).infos + +# Write numerical parameter estimated values: +output.estimates = $(DATA).params.txt + +# ---------------------------------------------------------------------------------------- +# Bootstrap +# ---------------------------------------------------------------------------------------- + +bootstrap.number = 0 +# Tell if numerical parameters should be kept to their initial value when bootstrapping: +bootstrap.approximate = no +# Set this to yes for detailed output when bootstrapping. +bootstrap.verbose = no +bootstrap.output.file = $(DATA).ML_bstrees.dnd + diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Nucleotides/Homogeneous/ML.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Nucleotides/Homogeneous/ML.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Nucleotides/Homogeneous/ML.bpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Nucleotides/Homogeneous/ML.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -1,5 +1,5 @@ -#initial logL: -65639.1410465442 -#final logL: -65442.8035360931 +#initial logL: -65826.8571771722 +#final logL: -65428.449112789 # Global variables: DATA = LSU @@ -39,7 +39,7 @@ # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # -model = HKY85(kappa=2.843, theta=0.5, theta1=0.5, theta2=0.5, useObservedFrequencies=yes) +model = HKY85(kappa=2.843, initFreqs=observed) rate_distribution = Gamma(n=4, alpha=0.358) diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/MLNH.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/MLNH.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/MLNH.bpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/MLNH.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -1,11 +1,20 @@ -#Initial log likelihood.................: -71011.8177084265 -#Log likelihood.........................: -65343.8442233959 -#GC.theta...............................: 0.483464 -#T92.kappa_1............................: 2.63716 -#T92.theta_1............................: 0.576654 -#T92.theta_2............................: 0.445837 -#Gamma.alpha............................: 0.439279 -#111.83user 0.07system 1:52.90elapsed 99%CPU +#Initial log likelihood.................: -67066.6981049241 +#Log likelihood.........................: -65187.3822910926 +#Full.theta.............................: 0.481587 +#Full.theta1............................: 0.568231 +#Full.theta2............................: 0.591547 +#GTR.a_1................................: 1.27372 +#GTR.b_1................................: 0.667001 +#GTR.c_1................................: 0.344267 +#GTR.d_1................................: 0.339924 +#GTR.e_1................................: 0.37557 +#GTR.theta_1............................: 0.622987 +#GTR.theta1_1...........................: 0.469133 +#GTR.theta2_1...........................: 0.547965 +#GTR.theta_2............................: 0.491549 +#GTR.theta1_2...........................: 0.485613 +#GTR.theta2_2...........................: 0.555095 +#Gamma.alpha............................: 0.438647 # Global variables: @@ -60,7 +69,7 @@ nonhomogeneous.number_of_models = 2 # Set up each model: -model1 = GTR(theta=0.5, useObservedFreqs=yes) +model1 = GTR(initFreqs=observed) model1.nodes_id=0:62 # The Ids of the nodes to which this model should be assigned. model2 = GTR(a=model1.GTR.a,\ @@ -68,7 +77,7 @@ c=model1.GTR.c,\ d=model1.GTR.d,\ e=model1.GTR.e,\ - theta=0.9, useObservedFreqs=yes) + initFreqs=observed) model2.nodes_id=63:154 # Likelihood recursion option: @@ -93,7 +102,7 @@ optimization=FullD(derivatives=Newton) optimization.reparametrization=no optimization.verbose = 1 -optimization.ignore_parameter = RootPosition +optimization.ignore_parameter = optimization.max_number_f_eval = 10000 optimization.tolerance = 0.000001 optimization.message_handler = $(DATA).messages diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/MLNHGG.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/MLNHGG.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/MLNHGG.bpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/MLNHGG.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -1,11 +1,11 @@ #Initial log likelihood.................: -65639.1410465442 -#Log likelihood.........................: -64547.3493038365 +#Log likelihood.........................: -64547.3486924172 #GC.theta...............................: 0.486755 #T92.theta_1............................: 0.438231 -#T92.theta_2............................: 0.778319 +#T92.theta_2............................: 0.778332 #etc -#Gamma.alpha............................: 0.43608 -#1566.56user 0.36system 26:13.49elapsed 99%CPU +#Gamma.alpha............................: 0.436095 +#2621.12user 0.63system 43:47.81elapsed 99%CPU # Global variables: diff -Nru bppsuite-0.6.2/Examples/MaximumLikelihood/Proteins/Homogeneous/ML.bpp bppsuite-0.7.0/Examples/MaximumLikelihood/Proteins/Homogeneous/ML.bpp --- bppsuite-0.6.2/Examples/MaximumLikelihood/Proteins/Homogeneous/ML.bpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/MaximumLikelihood/Proteins/Homogeneous/ML.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -1,5 +1,5 @@ -#initial logL: -5140.62864568291 -#final logL: +#initial logL: -5140.62856257665 +#final logL: -4958.52926533168 # Global variables: DATA = Myo @@ -39,7 +39,7 @@ # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # -model = JTT92+F(useObservedFreqs=yes) +model = JTT92+F(initFreqs=observed, initFreqs.observedPseudoCount=0.) rate_distribution = Gamma(n=4, alpha=0.5) diff -Nru bppsuite-0.6.2/Examples/README bppsuite-0.7.0/Examples/README --- bppsuite-0.6.2/Examples/README 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/README 2012-02-15 22:04:28.000000000 +0000 @@ -8,6 +8,10 @@ treeList.dnd A list of trees in newick format. treeList2.dnd Another list of trees in newick format. OutGroup.txt A list of taxons to be used with BppReRoot. + lysozymeLarge.fasta and .dnd Files from the PAML package. + Myo.mase Myoglobin sequence alignment, From dutheil and Galtier 2007 + HIV1_REF_2010_gag_DNA.fasta Alignment file downloaded from the HIV database on 21/12/11 + " " _macse realigned with Macse 0.8 ..:: Options files ::.. @@ -25,4 +29,5 @@ SeqMan.bpp BppSeqMan option file. PhySamp.bpp BppPhyloSampler option file. ReRoot.bpp BppReRoot option file. + AlnScores.bpp BppAlnscore option file. diff -Nru bppsuite-0.6.2/Examples/SequenceManipulation/SeqMan2.bpp bppsuite-0.7.0/Examples/SequenceManipulation/SeqMan2.bpp --- bppsuite-0.6.2/Examples/SequenceManipulation/SeqMan2.bpp 1970-01-01 00:00:00.000000000 +0000 +++ bppsuite-0.7.0/Examples/SequenceManipulation/SeqMan2.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -0,0 +1,33 @@ +# Global variables: +DATA = HIV1_REF_2010_gag + +# --------------- +# Input sequences +# --------------- + +# The alphabet to use: +# [DNA|RNA|Protein|Generic] +alphabet=Codon(code=Standard, letter=DNA) + +# The sequence file to use (sequences must be aligned!) +input.sequence.file=../Data/$(DATA)_DNA.fasta + +# The file format: +input.sequence.format=Fasta + +# ---------------- +# Output sequences +# ---------------- + +output.sequence.file=$(DATA)_AA.fasta + +# The file format: +output.sequence.format=Fasta() + +# ----------------------- +# Sequences manipulations +# ----------------------- +#For example (see manual for a detailed list of available options): +sequence.manip = CoerceToAlignment,RemoveStops,KeepComplete(maxGapAllowed=30%),Translate(code=StandardGeneticCode) + + diff -Nru bppsuite-0.6.2/Examples/SequenceSimulation/SeqGen.bpp bppsuite-0.7.0/Examples/SequenceSimulation/SeqGen.bpp --- bppsuite-0.6.2/Examples/SequenceSimulation/SeqGen.bpp 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/Examples/SequenceSimulation/SeqGen.bpp 2012-02-15 22:04:28.000000000 +0000 @@ -4,7 +4,7 @@ # Input tree to use: input.tree.file = ../Data/LSUrooted.dnd -input.tree.Format=Newick +input.tree.format=Newick # Print a tree with ids as bootstrap values. # This is helpful when setting up complexe non-homogeneous models. diff -Nru bppsuite-0.6.2/.git/FETCH_HEAD bppsuite-0.7.0/.git/FETCH_HEAD --- bppsuite-0.6.2/.git/FETCH_HEAD 2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/.git/FETCH_HEAD 2012-02-15 22:04:28.000000000 +0000 @@ -1 +1 @@ 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2011-06-16 12:33:02.000000000 +0000 +++ bppsuite-0.7.0/man/CMakeLists.txt 2012-02-15 22:04:28.000000000 +0000 @@ -13,4 +13,5 @@ INSTALL(FILES bppreroot.1.gz DESTINATION share/man/man1) INSTALL(FILES bppphysamp.1.gz DESTINATION share/man/man1) INSTALL(FILES bpptreedraw.1.gz DESTINATION share/man/man1) + INSTALL(FILES bppalnscore.1.gz DESTINATION share/man/man1) ENDIF(MAN)