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Pages matching "phyml" in Launchpad

116 of 17 pages matching "phyml"
  • Change log for arb package in Debian. ... 60_use_debian_phyml use phyml from debian package for both interfaces in ARB * debian/rules: - create config.makefile from override_dh_configure target - use "make tarfile" in override_dh_install - remove extra cleaning not needed for ARB 6 - use "dh_install --list-missing" to avoid missing files ...
  • First beta release which contains all the functionality of the old STK, plus Safe Taxonomic Reduction, Matrix partitioning and be packaged for Ubuntu, etc.
  • The following packages are available in Bio-Linux 8, but absent from this PPA, as they are updated in the Ubuntu 16.04 repos: abyss ampliconnoise arb bamtools bedtools bowtie bowtie-examples bowtie2 bowtie2-examples bwa clearcut duplicity duply ea-utils emboss emboss-d...
  • Multiple substitution stages lead to incorrect final subs Bug #1333749 reported by Jon Hill on 2014-06-24. 6. This bug affects 1 person. Affects Status Importance Assigned to ... 2 store the full subs history in the Phyml so we can do the above automagically 3 carry out substitutions on a subs file (i.e. the RHS, which has no structure) and ...
  • Other issues here: - existing tests check tree names, etc, but these are not in the data right now. Do we add the names to each Phyml in the dataset?
  • Hello when I open my phyml file, I keep having, on top of the usual Warning about added xml attributes, a warning telling me: Warning: lost xml elements: <comment>Unsure whether the authors used Maximum Likelihood or Maximum Parsimony</comment> <comment>Unsure whether the authors used Maximum Likelihood or Maximum Parsimony</comment> This relates to a comment I added on the comment section of ...
  • Phyml is a bit of software and anything Phy seems to have phylogenetic connotations, rather than being supertree only. stkml might work well!
  • stk/supertree_toolkit.py (+5/-2) stk_gui/gui/gui.glade (+17/-1) stk_gui/plugins/phyml/import_tree.py (+5/-1) stk_gui/stk_gui/interface.py (+19/-13)
  • File "/usr/share/ plugins/ phyml/import_ tree.py", line 42, in handle_click tree_name = stk.create_ tree_name(xml,element[0].get_ parent().get_parent()) AttributeError: 'lxml.etree. _Element' object has no attribute 'get_parent' This is getting the source. Note the source name hadn't been set at this point.
  • I can't replicate this - can you attach the PHYML, and let me know what you searched for, please? Katie Davis (k-davis) wrote on 2013-09-10 : Re: [Bug 1222814] Re: "find" function crashes gui and wipes entire file
  • Performing a large substitution with the GUI results in: jhill1@rheic ~/Desktop $ stk-gui SupertreeKD.phyml /usr/bin/ stk-gui: 263: PangoWarning: Invalid UTF-8 string passed to pango_layout_ set_text() gtk.main() Traceback (most recent call last):
  • When I click on Data summary, I get an error: Failed to summarise data. Taxon: Geropteron is not in the tree Bybee_etal_2008_4 Taxon: TupusMegatypus is not in the tree Bybee_etal_2008_4
  • The tree below does not parse. The UTF “ “ do not parse in p4? #NEXUS [File saved Fri Aug 16 20:23:39 2013] BEGIN TAXA; DIMENSIONS NTAX = 68;
  • Report: Traceback (most recent call last): File "/usr/local/ lib/python2. 7/dist-packages/ stk_gui/ interface. py", line 1951, in on_export_ trees_save ignoreWarnings ...
  • Both characters and analysis default to an option are therefore "correctly filled in" when a new source is added. They should be "blue" by default, with a blank entry.
  • Please backport autoconf 2.69-6 (main) from trusty to precise. Reason for the backport: ===== It is the required packages for backporting pcsc-lite, ccid and acsccid. Testing: ===== Mark off items in the checklist [X] as you test them, but please leave the checklist so that backporters can quickly evaluate the state of testing.
116 of 17 pages matching "phyml"