--- boxshade-3.1.1.orig/makefile.unx +++ boxshade-3.1.1/makefile.unx @@ -40,3 +40,8 @@ dv_ps$(OBJ): dv_ps.c bx_types.h bx_read.h dv_all.h version.h dv_regis$(OBJ): dv_regis.c bx_types.h bx_read.h dv_all.h dv_rtf$(OBJ): dv_rtf.c bx_types.h bx_read.h dv_all.h + +.PHONY: clean + +clean: + rm -f $(OBJS) boxshade$(EXE) --- boxshade-3.1.1.orig/debian/README.Debian +++ boxshade-3.1.1/debian/README.Debian @@ -0,0 +1,11 @@ +boxshade for Debian +------------------- + +The web interface for boxshare is available for download +on ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/www/box_www.tar.Z + +It is not yet debinanised, please request this package and +explain your demand for it or use it on +http://www.ch.embnet.org/software/BOX_form.html + + -- Steffen Moeller , Sun, 29 Feb 2004 13:17:22 +0100 --- boxshade-3.1.1.orig/debian/changelog +++ boxshade-3.1.1/debian/changelog @@ -0,0 +1,6 @@ +boxshade (3.1.1-1) unstable; urgency=low + + * Initial Release (Closes: #234923). + + -- Steffen Moeller Thu, 26 Feb 2004 13:17:22 +0100 + --- boxshade-3.1.1.orig/debian/boxshade.xml +++ boxshade-3.1.1/debian/boxshade.xml @@ -0,0 +1,358 @@ + +.
will be generated. You may view the +manual page with: nroff -man .
| less'. A +typical entry in a Makefile or Makefile.am is: + +DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\ +manpages/docbook.xsl +XP=xsltproc -''-nonet + +manpage.1: manpage.dbk + $(XP) $(DB2MAN) $< + +The xsltproc binary is found in the xsltproc package. The +XSL files are in docbook-xsl. Please remember that if you +create the nroff version in one of the debian/rules file +targets (such as build), you will need to include xsltproc +and docbook-xsl in your Build-Depends control field. + +--> + + + Steffen"> + Möller"> + + February 26, 2004"> + + 1"> + moeller@pzr.uni-rostock.de"> + + BOXSHADE"> + + + Debian"> + GNU"> + GPL"> +]> + + + +
+ &dhemail; +
+ + &dhfirstname; + &dhsurname; + + + 2003 + &dhusername; + + &dhdate; + + + &dhucpackage; + + &dhsection; + + + &dhpackage; + + Pretty-printing of multiple sequence alignments + + + + &dhpackage; + + + + DESCRIPTION + BOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE. + + This manual page was written for the &debian; distribution + because the original program does not have a manual page. The presented information comes from the documentation of the Web Service of the 3.21 version that is not available as a Debian package. + + + +BOXSHADE is a program for creating good looking printouts from +multiple-aligned protein or DNA sequences. The program does no alignment +by itself, it has to take as input a file preprocessed by a multiple +alignment program or a multiple file editor. See below for a list of +supported input formats and output devices. In the standard BOXSHADE +output, identical and similar residues in the multiple-alignment chart +are represented by different colors or shadings. There are some more +options concerning the kind of shading to be applied, sequence numbering, +consensus output and so on. The user interface is a bit clumsy at +the moment, one has to answer a lot of questions in order to get the +desired output. There is, however, the possibility to use default +parameters from a standard parameter file or to supply the program +with parameters from the command line. At the moment, the VMS and DOS +versions of BOXSHADE have identical user interfaces. + +- Input formats - + +BOXSHADE 3.2 knows about the following input file formats: (some of +the are generally used only for MSDOS or VMS systems) + CLUSTAL and +CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension .ALN ++ ESEE, multiple sequence editor, DOS default extension .ESE + PHYLIP, +phylogenetic analysis package, DOS, VMS, UNIX default extension .PHY + +PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX default +extensions .MSF and .PRE NB!! you are strongly encouraged NOT to use the +PRETTY format as input, it may be incompatible with the revised version +of .MSF input. We can't actually think why anyone would use this format +now, .MSF files are more useful generally. + MALIGNED, multiple sequence +editor, VMS only default extension .MAL BOXSHADE tries to determine the +file type from the extension but will work also if different extensions +are used. + + - Output devices - +POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on +a Laserprinter or for further conversion with a POSTCRIPT interpreter +(like GHOSTSCRIPT) + HPGL for export to various graphics programs or +for conversion/printing with the shareware program PRINTGL. Plotting +BOXSHADE output on a plotter is generally not recommended + RTF for +export to various word-processing and graphics programs + CRT, uses direct +screen writes to the PC-monitor. Possible options depend on the graphics +adapter used. This output device is supported only in the MSDOS version. + +ANSI. On a PC, this option uses an ANSI device driver (ANSI.SYS) that has +to be loaded in CONFIG.SYS previously. Possible character renditions are +reverse, bold,underlined, blinking etc. On non-DOS systems, this option +behaves more or less like the VT100 output mode. + VT100 for display on a +VT100 compatible terminal or emulator. + ReGISterm for display on a ReGIS +compatible graphics terminal or emulator. + ReGISfile for later conversion +by the program RETOS (copyright DEC) in order to print on DIGITALs +printer series. + LJ250 for printing on DIGITALS LJ250 color printer. + +ASCII output showing either the conserved residues or the varying ones +(others as '-'). + FIG file for xfig 2.1. + PICT files for import to Mac +and PC graphics progs. Some of the formats above offer the possibility +of scaling the characters and of rotating the plot. Character size has +to be entered in 'point' units. Normal output orientation is in portrait +mode (PS/EPS/HPGL/PICT only), to obtain output in landscape orientation, +'rotate plot = y' has to be chosen. When creating multi-page output, +all pages are contained in a single output file. If one page per file +is desired, one has to use the command line parameter /SPLIT. This is +enforced when requesting EPSF or PICT file output, as multi-page EPSFs +are a contradiction of the purpose of an EPSF and large PICT files would +probably be too big for most personal computers. While using the terminal +as output device, the 'RETURN' key has to be pressed to obtain the next +page of output. + +- Sequence numbering - +Starting with version 2.2 there +is the possibility to add numbering to the output files. The numbers are +printed between the sequence names and the sequence itself. Since most of +the input-files either use no numbering or number the first position in +the alignment always with a "1" (and that does not necessarily reflect +the numbers within the original sequence), the user is asked to enter +the starting position for each sequence. The command line flag /DEFNUM +suppressed that question, a starting position of 1 is assumed for all +sequences. Boxshade starts with the value entered for the leftmost +position and continues numbering every valid symbol, skipping blanks, +'-','.' and stuff like that. + +- Default parameters - +Several people using +previous releases of BOXSHADE pointed me to the need of having default +parameters for the various questions asked by the program. They argued +that most sites only use one type of input files, one output device and +one choice of colors for the output. I therefore added a management of +default parameters allowing two levels of assistance to the user. 1) all +default parameters are contained in an ASCII file that can be modified +easily to accomodate the users taste. The format is roughly documented +within the file-header, it resembles the keyboard input one has to make +if using the program interactively. There are two such files supplied +with this release of BOXSHADE, BOX_DNA.PAR and BOX_PEP.PAR , holding +some example parameters for peptide and dna-comparisons. there are no +big differences between these two, the major one is that when shading +DNA-comparisons one doesn't care of "similar" residues. 2) to run the +program with minimal user interaction, I have added the possibility to +use command line parameters. At the moment, you can use: /check : list +all allowed command line paramters (this list) and allows parameters to +be added. /def : program runs without questions, BOX_PEP.PAR is used as +default /dna : makes the program use BOX_DNA.PAR as parameter file /pep : +makes the program use BOX_PEP.PAR as parameter file /in=xxx : makes the +program take xxx as input file /out=yyy : makes the program take yyy as +output file (note1) /par=zzz : makes the program use zzz as a default +parameter file /type=1 : makes the program assume an input file of type +1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of +type 1 (CRT) /numdef : use default numbering (all sequences starting +with "1") /thr : threshold fraction of residues that must agree for a +consensus /split : forces one page per file output, creates multiple +output files. /cons : makes the program create an additional consensus +line (see below) /symbcons=: influences the way the consensus line is +displayed. (see below) /unix : writes output files in unix style (LF only) +(note2) /dos : writes output files in DOS style (CR/LF) (note2) note1: +on unix machines, use out=OUTPUT for terminal output on DOS machines, +use out=con: on VMS machines, use out=tt: note2: if no mode is specified, +the native style of the machine is used. + +ATTENTION +on unix systems, the dash (-) instead of the slash (/) has to be used as separation character for command line paramters. For example, a valid unix command line is: boxshade -def -numdef -cons -symbcons=" .*" ************************************************************************** + +- Shading strategies (similarity to consensus or single sequence) - + +Starting with version 3, BOXSHADE has a new shading system. The first +difference is the introduction of a threshold fraction of residues that +must agree for there to be a consensus. Previously, the program assumed +that SOME residue was always the consensus. If no two residues were the +same, the first sequence provided the consensus residue. This threshold +fraction can be any number between 0.0 and 1.0. The number of sequences +that must agree for there to be a consensus is, as you might expect, +this fraction times the total number of sequences in the alignment +(fractions of a sequence count as one, e.g. 3.2 becomes 4). The second +difference is the idea of 'consensus by similarity'; this tries to take +account of the situations where all the sequences may have (for example) +R or K at a position, but neither in a majority. It would not be logical +to shade one type of residue as 'identical' and the other as 'similar'; +the threshold function might also eliminate both as being in too small +numbers. Therefore, if there is not a single residue that is conserved +(greater than the threshold) at a position, the program looks for a +'group' of amino acids that fulfills the requirements. 'Groups' are +defined in the .grp files. Users can tailor these to their personal +prejudices. Any amino acid not listed is assumed not to be in a group. All +members of a group are considered to be mutually similar, unlike the +.sim files, described below. If consensus by similarity is found, all the +residues in the consensus are shaded using the 'similar' shading defined +by the user. If the user does not select 'shading by similarity', only +identity-type consensus is looked at. If an identity-type consensus is +found, and similarity shading is in operation, the program looks to see +if the remaining residues are similar to the consensus residue. Here the +box_xxx.sim files are used. The main difference between relationships +in these files and those in the .grp files is that, e.g. in a .grp +file the line STA means that all three a.a.s are mutually similar. In +a .sim file S TA means that both T and A are considered similar to S, +where there is a conserved S residue in more than threshold number of +sequences. However, it does NOT mean that T and A are similar to each +other. Note that cases where two residues, or groups of residues, +fulfill the threshold requirements (as could happen with values of +the thr. fraction less than or equal to 0.5) are treated as having no +consensus. This describes the main shading model 'shading according to +a consensus'. The alternative model is called 'shading according to +a master sequence'. In this case the user is prompted for a sequence +of the alignment and consecutively that sequence is taken to be the +'consensus'. Only those residues become shaded that are identical or +similar to the chosen sequence. Output obtained with this option tends +to be less shaded and neglects similarities beween the other (non-chosen) +sequences. Starting in V2.7, this 'master sequence' can be hidden. Thus, +it only influences the shading of the other sequences without being +shown itself. + +- Consensus display - +Starting with version 2.5, BOXSHADE +offers the possibility to create an additional line holding a consensus +symbol. This line can either be obtained by using the command line +qualifier /CONS or interactively by answering the question ' create +consensus? '. The way this consensus line is displayed can be modified +by the command line parameter SYMBCONS=xyz, by editing the respecitve +entry in the .PAR file or interactively. Since the SYMBCONS syntax is +not intuitive, here a brief description: The SYMBCONS parameter consist +of exactly three symbols: + the first one stands for 'normal' sequence +residues that are not involved in any similar/identical relationship. + +the second symbol represents positions that are similar in all sequences +of the alignment. See the files BOX_PEP.SIM and BOX_DNA.SIM to see +what residues are considered similar. + the third symbol represents +positions that are identical in all sequences of the alignment. A +SYMBCONS parameter string " .*" (blank/point/asterisc) means: label +all positions in the alignment with totally identical residues by an +asterisc, all positions with all similar residues by a point and do not +mark the other positions. The letter 'B' can be used instead of the blank, +this is necessary e.g. when using the command line option /SYMBCONS=B.* +which gives the same result as the above example. The option /SYMBCONS= +.* would result in an unexpected behaviour because MSDOS squeezes blanks +out of the command line. Besides points, asteriscs and other symbols, +there are two special characters when they appear in the SYMBCONS string: +'L' and 'U'. An 'L' means, that a lowercase representation of the +most abundant residue at that position is to be used instead of a fixed +consensus symbol while an 'U' means an uppercase character representation +of that residue. A possible application would be the SYMBCONS string " +LU" where similar residues are represented by lowercase characters and +identical by uppercase characters. + + +- shareware/PD programs useful in conjunction with BOXSHADE - + + +multiple alignment files that to be used by BOXSHADE can be created, +amongst others, by the following PD/freeware programs: + PHYLIP by Joe +Felsenstein, available by ftp from anthro.utah.edu + ESEE by Eric Cabot, +available from the same sources as BOXSHADE (see above) + CLUSTAL by Des +Higgins, ditto for preview/conversion of POSTSCRIPT files, the program +GHOSTSCRIPT from GNU software foundation is highly recommended. It is +available from all major MSDOS ftp-sites (e.g. SIMTEL or ftp.uni-koeln.de) +There is also a version tested for use with boxshade available at +vax0.biomed.uni-koeln.de although this might be not the most recent +release. for Mac users, there is MacGhostscript, also available from the +main archives (info-mac, umich and their mirrors). A *very* good tool +for putting a preview image into an EPSF file, often a prerequisite for +incorporating into a drawing package, is PS2EPS, by Peter Lerup. This can +be found on info-mac. for preview/conversion of HPGL files, the shareware +program PRINTGL 1.18 by Cary Ravitz is highly recommended. It is available +from many MSDOS ftp sites and from netserv@embl-heidelberg.de - output on +dot printers - Since PRINTGL offers a broad choice of printer types and +is a nice program, I recommend its use for printing BOXSHADE output on +non-POSTSCRIPT printers. Use HPGL output with options 0F1N for normal +residues 2F1N for identical residues 3F1N for similar residues 2F4N +for conserved residues 8 for character size not rotated (these are the +standard parameters in BOX_PEP.PAR) for creating a HPGL files. (lets call +it TEST.PLT) Now use PRINTGL either interactively by calling PMI or use +a command line like: PRINTGL /Fx/S0340/Waaac/Ptest.plt where test.plt is +to be replaced by the filename to convert and the x in the expression +/Fx is to be replaced by the letter of the printer you use. (See the +PRINTGL documentation for further details) + + + +RESTRICTIONS + + +The RTF output and PHYLIP input implementations are still +experimental. Please tell me of your experiences with the program. + +the current DOS version supports only 13 sequences with 2000 residues +each. This parameters can be easily changed in the source code. If you +cannot compile the sources because you are lacking a pascal compiler, +contact the author for precompiled versions + +DISTRIBUTION POLICY + +BOXSHADE is completely public-domain and may be passed around and modified without any notice to the author. If you have problems, suggestions or remarks, please contact either of us: +Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848 +MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany +E-mail: Kay.Hofmann@memorec.com +Michael D. Baron Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U.K. +E-mail: michael.baron@bbsrc.ac.uk + + + + SEE ALSO + + /etc/boxshade/*.par + seaview (1), + clustalw (1) + + + + AUTHOR + + This manual page was written by &dhusername; &dhemail; for + the &debian; system (but may be used by others). Permission is + granted to copy, distribute and/or modify this document under + the terms of the &gnu; General Public License, Version 2 any + later version published by the Free Software Foundation. + + + On Debian systems, the complete text of the GNU General Public + License can be found in /usr/share/common-licenses/GPL. + + + + + --- boxshade-3.1.1.orig/debian/compat +++ boxshade-3.1.1/debian/compat @@ -0,0 +1 @@ +4 --- boxshade-3.1.1.orig/debian/control +++ boxshade-3.1.1/debian/control @@ -0,0 +1,18 @@ +Source: boxshade +Section: science +Priority: extra +Maintainer: Steffen Moeller +Build-Depends: debhelper (>= 4.0.0), xsltproc, docbook-xsl, docbook-xml +Standards-Version: 3.6.0 + +Package: boxshade +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: seaview, clustalw, xfig +Description: [Biology] Pretty-printing of multiple sequence alignments + Boxshade reads a sequence alignment as input (e.g. from ClustalW) and + outputs files that may be incorporated to text processing software + (TeX via xfig, Word and OpenOffice via RTF). The post script format + is also supported. + . + Homepage: http://www.ch.embnet.org/software/BOX_form.html --- boxshade-3.1.1.orig/debian/dirs +++ boxshade-3.1.1/debian/dirs @@ -0,0 +1,2 @@ +usr/bin +usr/sbin --- boxshade-3.1.1.orig/debian/menu +++ boxshade-3.1.1/debian/menu @@ -0,0 +1,6 @@ +?package(boxshade):\ + needs="text"\ + section="Apps/Science"\ + title="Boxshade"\ + command="/usr/bin/boxshade" + --- boxshade-3.1.1.orig/debian/rules +++ boxshade-3.1.1/debian/rules @@ -0,0 +1,109 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# GNU copyright 1997 to 1999 by Joey Hess. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + + + + +CFLAGS = -Wall -g + +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) + CFLAGS += -O0 +else + CFLAGS += -O2 +endif +ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS))) + INSTALL_PROGRAM += -s +endif + +configure: configure-stamp +configure-stamp: + dh_testdir + # Add here commands to configure the package. + + touch configure-stamp + + +build: build-stamp + +DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl +XP=xsltproc -''-nonet + +boxshade.1: debian/boxshade.xml + $(XP) $(DB2MAN) $< + + +build-stamp: configure-stamp boxshade.1 + dh_testdir + + # Add here commands to compile the package. + $(MAKE) -f makefile.unx + touch build-stamp + +clean: + dh_testdir + dh_testroot + rm -f build-stamp configure-stamp + + # Add here commands to clean up after the build process. + -$(MAKE) -f makefile.unx clean + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + # Add here commands to install the package into debian/boxshade. + mkdir -p $(CURDIR)/debian/boxshade/usr/bin \ + $(CURDIR)/debian/boxshade/usr/lib/boxshade \ + $(CURDIR)/debian/boxshade/etc/boxshade || true + + cp boxshade.sh $(CURDIR)/debian/boxshade/usr/bin/boxshade + cp boxshade $(CURDIR)/debian/boxshade/usr/lib/boxshade + cp *.grp *.par *.sim $(CURDIR)/debian/boxshade/etc/boxshade + + +# Build architecture-independent files here. +binary-indep: build install +# We have nothing to do by default. + +# Build architecture-dependent files here. +binary-arch: build install + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs +# dh_installexamples +# dh_install + dh_installmenu +# dh_installdebconf +# dh_installlogrotate +# dh_installemacsen +# dh_installpam +# dh_installmime +# dh_installinit +# dh_installcron +# dh_installinfo + dh_installman + dh_link + dh_strip + dh_compress + dh_fixperms +# dh_perl +# dh_python +# dh_makeshlibs + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install configure --- boxshade-3.1.1.orig/debian/copyright +++ boxshade-3.1.1/debian/copyright @@ -0,0 +1,12 @@ +This package was debianized by Steffen Moeller on +Thu, 26 Feb 2004 13:17:22 +0100. + +It was downloaded from: ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/ + +Upstream Authors: Kay Hofmann (kay.hofmann@memorec.de), Michael Baron (michael.baron@bbsrc.ac.uk), Hartmut Schirmer + +Copyright: + + No license restrictions. In a personal email from the 26th of February 2004 Kay Hofmann replied + "Das ganze Teil ist komplett public domain, Du kannst damit anstellen was immer du willst, ...". + that the software is completely public domain, allowing me to do with it whatever I want. --- boxshade-3.1.1.orig/debian/manpages +++ boxshade-3.1.1/debian/manpages @@ -0,0 +1 @@ +boxshade.1 --- boxshade-3.1.1.orig/boxshade.1 +++ boxshade-3.1.1/boxshade.1 @@ -0,0 +1,119 @@ +.\"Generated by db2man.xsl. Don't modify this, modify the source. +.de Sh \" Subsection +.br +.if t .Sp +.ne 5 +.PP +\fB\\$1\fR +.PP +.. +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Ip \" List item +.br +.ie \\n(.$>=3 .ne \\$3 +.el .ne 3 +.IP "\\$1" \\$2 +.. +.TH "BOXSHADE" 1 "February 26, 2004" "" "" +.SH NAME +boxshade \- Pretty-printing of multiple sequence alignments +.SH "SYNOPSIS" +.ad l +.hy 0 +.HP 9 +\fBboxshade\fR +.ad +.hy + +.SH "DESCRIPTION" + +.PP +\fBBOXSHADE\fR is a program for pretty\-printing multiple alignment output\&. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE\&. + +.PP +This manual page was written for the Debian™ distribution because the original program does not have a manual page\&. The presented information comes from the documentation of the Web Service of the 3\&.21 version that is not available as a Debian package\&. + +.PP +BOXSHADE is a program for creating good looking printouts from multiple\-aligned protein or DNA sequences\&. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor\&. See below for a list of supported input formats and output devices\&. In the standard BOXSHADE output, identical and similar residues in the multiple\-alignment chart are represented by different colors or shadings\&. There are some more options concerning the kind of shading to be applied, sequence numbering, consensus output and so on\&. The user interface is a bit clumsy at the moment, one has to answer a lot of questions in order to get the desired output\&. There is, however, the possibility to use default parameters from a standard parameter file or to supply the program with parameters from the command line\&. At the moment, the VMS and DOS versions of BOXSHADE have identical user interfaces\&. + +.PP +\- Input formats \- + +.PP +BOXSHADE 3\&.2 knows about the following input file formats: (some of the are generally used only for MSDOS or VMS systems) + CLUSTAL and CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension \&.ALN + ESEE, multiple sequence editor, DOS default extension \&.ESE + PHYLIP, phylogenetic analysis package, DOS, VMS, UNIX default extension \&.PHY + PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX default extensions \&.MSF and \&.PRE NB!! you are strongly encouraged NOT to use the PRETTY format as input, it may be incompatible with the revised version of \&.MSF input\&. We can't actually think why anyone would use this format now, \&.MSF files are more useful generally\&. + MALIGNED, multiple sequence editor, VMS only default extension \&.MAL BOXSHADE tries to determine the file type from the extension but will work also if different extensions are used\&. + +.PP +\- Output devices \- + +.PP +POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on a Laserprinter or for further conversion with a POSTCRIPT interpreter (like GHOSTSCRIPT) + HPGL for export to various graphics programs or for conversion/printing with the shareware program PRINTGL\&. Plotting BOXSHADE output on a plotter is generally not recommended + RTF for export to various word\-processing and graphics programs + CRT, uses direct screen writes to the PC\-monitor\&. Possible options depend on the graphics adapter used\&. This output device is supported only in the MSDOS version\&. + ANSI\&. On a PC, this option uses an ANSI device driver (ANSI\&.SYS) that has to be loaded in CONFIG\&.SYS previously\&. Possible character renditions are reverse, bold,underlined, blinking etc\&. On non\-DOS systems, this option behaves more or less like the VT100 output mode\&. + VT100 for display on a VT100 compatible terminal or emulator\&. + ReGISterm for display on a ReGIS compatible graphics terminal or emulator\&. + ReGISfile for later conversion by the program RETOS (copyright DEC) in order to print on DIGITALs printer series\&. + LJ250 for printing on DIGITALS LJ250 color printer\&. + ASCII output showing either the conserved residues or the varying ones (others as '\-')\&. + FIG file for xfig 2\&.1\&. + PICT files for import to Mac and PC graphics progs\&. Some of the formats above offer the possibility of scaling the characters and of rotating the plot\&. Character size has to be entered in 'point' units\&. Normal output orientation is in portrait mode (PS/EPS/HPGL/PICT only), to obtain output in landscape orientation, 'rotate plot = y' has to be chosen\&. When creating multi\-page output, all pages are contained in a single output file\&. If one page per file is desired, one has to use the command line parameter /SPLIT\&. This is enforced when requesting EPSF or PICT file output, as multi\-page EPSFs are a contradiction of the purpose of an EPSF and large PICT files would probably be too big for most personal computers\&. While using the terminal as output device, the 'RETURN' key has to be pressed to obtain the next page of output\&. + +.PP +\- Sequence numbering \- + +.PP +Starting with version 2\&.2 there is the possibility to add numbering to the output files\&. The numbers are printed between the sequence names and the sequence itself\&. Since most of the input\-files either use no numbering or number the first position in the alignment always with a "1" (and that does not necessarily reflect the numbers within the original sequence), the user is asked to enter the starting position for each sequence\&. The command line flag /DEFNUM suppressed that question, a starting position of 1 is assumed for all sequences\&. Boxshade starts with the value entered for the leftmost position and continues numbering every valid symbol, skipping blanks, '\-','\&.' and stuff like that\&. + +.PP +\- Default parameters \- + +.PP +Several people using previous releases of BOXSHADE pointed me to the need of having default parameters for the various questions asked by the program\&. They argued that most sites only use one type of input files, one output device and one choice of colors for the output\&. I therefore added a management of default parameters allowing two levels of assistance to the user\&. 1) all default parameters are contained in an ASCII file that can be modified easily to accomodate the users taste\&. The format is roughly documented within the file\-header, it resembles the keyboard input one has to make if using the program interactively\&. There are two such files supplied with this release of BOXSHADE, BOX_DNA\&.PAR and BOX_PEP\&.PAR , holding some example parameters for peptide and dna\-comparisons\&. there are no big differences between these two, the major one is that when shading DNA\-comparisons one doesn't care of "similar" residues\&. 2) to run the program with minimal user interaction, I have added the possibility to use command line parameters\&. At the moment, you can use: /check : list all allowed command line paramters (this list) and allows parameters to be added\&. /def : program runs without questions, BOX_PEP\&.PAR is used as default /dna : makes the program use BOX_DNA\&.PAR as parameter file /pep : makes the program use BOX_PEP\&.PAR as parameter file /in=xxx : makes the program take xxx as input file /out=yyy : makes the program take yyy as output file (note1) /par=zzz : makes the program use zzz as a default parameter file /type=1 : makes the program assume an input file of type 1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of type 1 (CRT) /numdef : use default numbering (all sequences starting with "1") /thr : threshold fraction of residues that must agree for a consensus /split : forces one page per file output, creates multiple output files\&. /cons : makes the program create an additional consensus line (see below) /symbcons=: influences the way the consensus line is displayed\&. (see below) /unix : writes output files in unix style (LF only) (note2) /dos : writes output files in DOS style (CR/LF) (note2) note1: on unix machines, use out=OUTPUT for terminal output on DOS machines, use out=con: on VMS machines, use out=tt: note2: if no mode is specified, the native style of the machine is used\&. + +.PP +ATTENTION + +.PP +on unix systems, the dash (\-) instead of the slash (/) has to be used as separation character for command line paramters\&. For example, a valid unix command line is: \fBboxshade \-def \-numdef \-cons \-symbcons=" \&.*" **************************************************************************\fR + +.PP +\- Shading strategies (similarity to consensus or single sequence) \- + +.PP +Starting with version 3, BOXSHADE has a new shading system\&. The first difference is the introduction of a threshold fraction of residues that must agree for there to be a consensus\&. Previously, the program assumed that SOME residue was always the consensus\&. If no two residues were the same, the first sequence provided the consensus residue\&. This threshold fraction can be any number between 0\&.0 and 1\&.0\&. The number of sequences that must agree for there to be a consensus is, as you might expect, this fraction times the total number of sequences in the alignment (fractions of a sequence count as one, e\&.g\&. 3\&.2 becomes 4)\&. The second difference is the idea of 'consensus by similarity'; this tries to take account of the situations where all the sequences may have (for example) R or K at a position, but neither in a majority\&. It would not be logical to shade one type of residue as 'identical' and the other as 'similar'; the threshold function might also eliminate both as being in too small numbers\&. Therefore, if there is not a single residue that is conserved (greater than the threshold) at a position, the program looks for a 'group' of amino acids that fulfills the requirements\&. 'Groups' are defined in the \&.grp files\&. Users can tailor these to their personal prejudices\&. Any amino acid not listed is assumed not to be in a group\&. All members of a group are considered to be mutually similar, unlike the \&.sim files, described below\&. If consensus by similarity is found, all the residues in the consensus are shaded using the 'similar' shading defined by the user\&. If the user does not select 'shading by similarity', only identity\-type consensus is looked at\&. If an identity\-type consensus is found, and similarity shading is in operation, the program looks to see if the remaining residues are similar to the consensus residue\&. Here the box_xxx\&.sim files are used\&. The main difference between relationships in these files and those in the \&.grp files is that, e\&.g\&. in a \&.grp file the line STA means that all three a\&.a\&.s are mutually similar\&. In a \&.sim file S TA means that both T and A are considered similar to S, where there is a conserved S residue in more than threshold number of sequences\&. However, it does NOT mean that T and A are similar to each other\&. Note that cases where two residues, or groups of residues, fulfill the threshold requirements (as could happen with values of the thr\&. fraction less than or equal to 0\&.5) are treated as having no consensus\&. This describes the main shading model 'shading according to a consensus'\&. The alternative model is called 'shading according to a master sequence'\&. In this case the user is prompted for a sequence of the alignment and consecutively that sequence is taken to be the 'consensus'\&. Only those residues become shaded that are identical or similar to the chosen sequence\&. Output obtained with this option tends to be less shaded and neglects similarities beween the other (non\-chosen) sequences\&. Starting in V2\&.7, this 'master sequence' can be hidden\&. Thus, it only influences the shading of the other sequences without being shown itself\&. + +.PP +\- Consensus display \- + +.PP +Starting with version 2\&.5, BOXSHADE offers the possibility to create an additional line holding a consensus symbol\&. This line can either be obtained by using the command line qualifier /CONS or interactively by answering the question ' create consensus? '\&. The way this consensus line is displayed can be modified by the command line parameter SYMBCONS=xyz, by editing the respecitve entry in the \&.PAR file or interactively\&. Since the SYMBCONS syntax is not intuitive, here a brief description: The SYMBCONS parameter consist of exactly three symbols: + the first one stands for 'normal' sequence residues that are not involved in any similar/identical relationship\&. + the second symbol represents positions that are similar in all sequences of the alignment\&. See the files BOX_PEP\&.SIM and BOX_DNA\&.SIM to see what residues are considered similar\&. + the third symbol represents positions that are identical in all sequences of the alignment\&. A SYMBCONS parameter string " \&.*" (blank/point/asterisc) means: label all positions in the alignment with totally identical residues by an asterisc, all positions with all similar residues by a point and do not mark the other positions\&. The letter 'B' can be used instead of the blank, this is necessary e\&.g\&. when using the command line option /SYMBCONS=B\&.* which gives the same result as the above example\&. The option /SYMBCONS= \&.* would result in an unexpected behaviour because MSDOS squeezes blanks out of the command line\&. Besides points, asteriscs and other symbols, there are two special characters when they appear in the SYMBCONS string: 'L' and 'U'\&. An 'L' means, that a lowercase representation of the most abundant residue at that position is to be used instead of a fixed consensus symbol while an 'U' means an uppercase character representation of that residue\&. A possible application would be the SYMBCONS string " LU" where similar residues are represented by lowercase characters and identical by uppercase characters\&. + +.PP +\- shareware/PD programs useful in conjunction with BOXSHADE \- + +.PP +multiple alignment files that to be used by BOXSHADE can be created, amongst others, by the following PD/freeware programs: + PHYLIP by Joe Felsenstein, available by ftp from anthro\&.utah\&.edu + ESEE by Eric Cabot, available from the same sources as BOXSHADE (see above) + CLUSTAL by Des Higgins, ditto for preview/conversion of POSTSCRIPT files, the program GHOSTSCRIPT from GNU software foundation is highly recommended\&. It is available from all major MSDOS ftp\-sites (e\&.g\&. SIMTEL or ftp\&.uni\-koeln\&.de) There is also a version tested for use with boxshade available at vax0\&.biomed\&.uni\-koeln\&.de although this might be not the most recent release\&. for Mac users, there is MacGhostscript, also available from the main archives (info\-mac, umich and their mirrors)\&. A *very* good tool for putting a preview image into an EPSF file, often a prerequisite for incorporating into a drawing package, is PS2EPS, by Peter Lerup\&. This can be found on info\-mac\&. for preview/conversion of HPGL files, the shareware program PRINTGL 1\&.18 by Cary Ravitz is highly recommended\&. It is available from many MSDOS ftp sites and from netserv@embl\-heidelberg\&.de \- output on dot printers \- Since PRINTGL offers a broad choice of printer types and is a nice program, I recommend its use for printing BOXSHADE output on non\-POSTSCRIPT printers\&. Use HPGL output with options 0F1N for normal residues 2F1N for identical residues 3F1N for similar residues 2F4N for conserved residues 8 for character size not rotated (these are the standard parameters in BOX_PEP\&.PAR) for creating a HPGL files\&. (lets call it TEST\&.PLT) Now use PRINTGL either interactively by calling PMI or use a command line like: PRINTGL /Fx/S0340/Waaac/Ptest\&.plt where test\&.plt is to be replaced by the filename to convert and the x in the expression /Fx is to be replaced by the letter of the printer you use\&. (See the PRINTGL documentation for further details) + +.SH " +RESTRICTIONS +" + +.PP +The RTF output and PHYLIP input implementations are still experimental\&. Please tell me of your experiences with the program\&. + the current DOS version supports only 13 sequences with 2000 residues each\&. This parameters can be easily changed in the source code\&. If you cannot compile the sources because you are lacking a pascal compiler, contact the author for precompiled versions + +.SH "DISTRIBUTION POLICY" + +.PP +BOXSHADE is completely public\-domain and may be passed around and modified without any notice to the author\&. If you have problems, suggestions or remarks, please contact either of us: Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848 MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany E\-mail: Kay\&.Hofmann@memorec\&.com Michael D\&. Baron Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U\&.K\&. E\-mail: michael\&.baron@bbsrc\&.ac\&.uk + +.SH "SEE ALSO" + +.PP +/etc/boxshade/*\&.par + +.PP +seaview (1), clustalw (1) + +.SH "AUTHOR" + +.PP +This manual page was written by Steffen Moeller for the Debian™ system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation\&. + +.PP +On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\&. + +.SH AUTHOR +Steffen Möller. --- boxshade-3.1.1.orig/boxshade.sh +++ boxshade-3.1.1/boxshade.sh @@ -0,0 +1,3 @@ +#!/bin/bash +export BOXDIR=/etc/boxshade +/usr/lib/boxshade/boxshade $*