debian/0000755000000000000000000000000011660647303007174 5ustar debian/clustalx.sharedmimeinfo0000644000000000000000000000100111660647277013751 0ustar Multiple sequence alignment in Clustal W format Alignement multiple de séquences au format Clustal W debian/watch0000644000000000000000000000015611660647277010241 0ustar version=3 opts=dversionmangle=s/\+lgpl// \ http://www.clustal.org/download/current/clustalx-([\.\d]*).tar.gz debian/README.source0000644000000000000000000000011111660647277011356 0ustar This package uses dpkg-source(1) to patch the original upstream sources. debian/control0000644000000000000000000000325611660647277010617 0ustar Source: clustalx Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 8), libqt4-dev Standards-Version: 3.9.2 Vcs-Browser: http://git.debian.org/?p=debian-med/clustalx.git Vcs-Git: git://git.debian.org/debian-med/clustalx.git Homepage: http://www.clustal.org/clustal2/ Package: clustalx Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: clustalw, texshade|texlive-latex-extra, boxshade Description: Multiple alignment of nucleic acid and protein sequences (graphical interface) This package offers a GUI interface for the Clustal multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated to highlight conserved features in the alignment. For professional presentations, one should use the texshade LaTeX package or boxshade. . The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment. . An alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. debian/CHANGELOG.upstream0000644000000000000000000002200511660647277012256 0ustar ---------------------------------------------------------------------- Version 2.1 ---------------------------------------------------------------------- * Fixed bug 196 "clustalx: user feedback about use of secondary structure printed to console" - secondary structure is now used if specified in Alignment -> Alignment Parameters -> Secondary Structure Parameters UserParameters->getGui() should be used when ClustalW code needs to know if a function has been called from ClustalX * Fixed bug 204 "Nexus alignment format contain invalid line" - the amino acid alphabet line has been removed * Missing/corrupted file names in ClustalX status messages have been fixed * Fixed bug 175 "msf/pileup files cannot be read if sequences names are all numbers" - this happened if a line such as 528244 .......... .......... .......... .......... .......... was present in the first block of the file * Fixed bug 192 "Alignment in Phylip Format broken for big Alignments" * Fixed bug 198 "Warning about divergent sequences gets printed to console in ClustalX" * Fixed bug 151 "clustalx doesn't switch to profile alignment mode when profile12 is given on cmdline" ---------------------------------------------------------------------- Version 2.0.12 ---------------------------------------------------------------------- * Fixed bug 189 "Fixed filename used for iteration": Now Creating temporary file and added error check * Fixed bug 180 "Pairwise NJ tree: final bracket missing" * Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity": Using relative error now to avoid unsafe comparison which led to incorrect branching * Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well" * Fixed bug 162 "percent identity file option in clustalW not working": Added -pim as command line option. See help * Fixed bug 155 "upgma trees cannot be read" * Fixed bug 147 "report duplicate sequences": "ClustalW/X now report offending sequences which are empty, duplicates etc * Fixed bug 134 "Exit when encountering unrecognized cmdline params": ClustalW now exits when encountering invalid values for command line arguments instead of just reverting to default values * Fixed bug 185 "clustal alignments differ between interactive and commandline mode" window-gap and ktuple initialisation now fixed and made the same between commandline and interactive mode * Fixed bug 184 "error messages are send to stdout" * Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA code (see RootedGuideTree.cpp) * General code cleanup - Introduced return values where control reached end of non-void function - Removed unused variables - Removed comparison between signed and unsigned integer expressions - Removed deprecated conversion from string constant to char* ---------------------------------------------------------------------- Version 2.0.11 ---------------------------------------------------------------------- * fixed file extension bug 166 in interactive mode * Fixed bug 169, memory violation for DNA/RNA k-tuple * Cut down distance calculation, symmetric matrix ---------------------------------------------------------------------- Version 2.0.10 ---------------------------------------------------------------------- * Fixed g++-4.3 compilation errors * Added new -quiet command line flag * Added new -stats= command line flag * Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms * Fixed bug 141: profile merging and saving failed * Fixed bug 139: saving of column quality scores * Updated help files (new flags, new colour parameter format) ---------------------------------------------------------------------- Version 2.0.9 ---------------------------------------------------------------------- * GUI now responding and giving feedback during alignment * automatic automake os detection * new OS_ define (set by clustalw/configure clustalx/clustalx.pro) * got rid of qt3 dependencies * removed QScrollArea bug workaround (fixed in Qt 4.3) * Fixed bug 135: Last sequence and last residue not displayed on MacOSX * Fixed bug 123: secondary structure profile alignment in clustalX on Mac * Fixed g++-4.3 build error (include climits.h) ---------------------------------------------------------------------- Version 2.0.8 ---------------------------------------------------------------------- * Implemented maxseqlen cmdline switch * Updated help-file * Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac) * Fixed bug 133: providing profiles on command line fails (ClustalX) * Fixed bug 125: Angle bracket inside sequence * Fixed bug 129: Early exit on empty sequence * Fixed a couple of possible memory leaks ---------------------------------------------------------------------- Version 2.0.7 ---------------------------------------------------------------------- * Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed * Fixed bug 122: convert option broken * Fixed reopened bug 114: profile alignment input didn't work with new getSeqRange routines * Fixed bug 119: build with g++ 4.3 ---------------------------------------------------------------------- Version 2.0.6 ---------------------------------------------------------------------- * Fixed bug 77: fasta input performance issue * Fixed bug 114: segfault while doing profile alignment with secondary structure mask * Removed unncessary id console output in EMBLFileParser.cpp * Fixed Bugs 108 and 109 and allowed mixed-case command line options ---------------------------------------------------------------------- Version 2.0.5 ---------------------------------------------------------------------- * Fixed bug 105: Disallowed combination of "Reset Gaps" and Iteration in GUI * Fixed bug 104 "reset all gaps doesn't work" * Changed command line separator for Mac to hyphen instead slash * Fixed full command line parsing for ClustalX after help flag ---------------------------------------------------------------------- Version 2.0.4 ---------------------------------------------------------------------- * Updated URLs in help files * Fixed bug 96: error message when loading alignment with identical sequence names * Made console output look more like 1.83 * Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83" getMatrix was called with wrong scaling factor * Fixed bug 99: "stars in input not ignored" Asterisks were changed to gaps in alignment * New command line option: -fullhelp which dumps the built-in help file content. * Quickfix for bug 94 "quicktree seqfault" ---------------------------------------------------------------------- <= Version 2.0.3 ---------------------------------------------------------------------- * Added LICENSE file to distribution This file contains the information about commercial licensing of clustal as well as FAQ for licensing issues * Added README file to distribution This is the file that lists the files and directories on the Clustal FTP site. It also includes acknowledgements of people who have contributed binaries * Removed .pro Qt file from the distribution pro-file should be generated anew using qmake and modified according to build requirements, i.e. no need for version control. * Fixed bug where ClustalX2 was not processing command line args * Fixed Segfault on opening helpfile. Happened on Linux only with -O2 and when calling binary directly, not using the wrapper * Added debian packaging files * Added support for help command line flag GUI/xmenus version When requesting help file, graphical version of command line help is displayed (1.83 tried to open clustalw help) * Added complete automake (configure etc) system according to the following websites: - http://www.openismus.com/documents/linux/automake/automake.shtml - http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html * clustalw files source files have been moved to subdir * Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30. This fixes problem of large amount of space between sequence name and actual alignment in clustal output files * This solves bug #72 with long lines (5000+) in fasta files changed code to use strings rather than arrays. Needed to add delim parameter to getline in order to read files formatted for different OSs on different platforms. * Fixed Bug 79: "The count of amino acids in the ClustalX Postscript output not correct" Off-by-one issue * ClustalX and ClustalW version numbers are now the same and defined in ClustalW code (automake) * Fixed problem with compilation of ClustalX2 with gcc3 avoiding gcc3 error message: cannot declare member function QDir::currentPath' * Target now clustalw2 instead of clustalw * Fixed Bug 46 added in aminoacid code O for pyrrolysine * Fixed bug 89 changed clustalw2.0 to conform to 1.83 behaviour for width of sequence ID and alignment * Fixed bug 90 changed clustalw2.0 to conform to 1.83 behaviour leading spaces are stripped from FASTA identifiers. * Fixed bug 91 Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out numbers and spaces. debian/changelog0000644000000000000000000002501311660647303011047 0ustar clustalx (2.1+lgpl-2) unstable; urgency=low [8b9662e] Update providing upgrade path to backports (Closes: #648812). [727f540] Corrected and normalised copyright file with config-edit. [fa455a0] Conforms to Policy version 3.9.2 (no changes needed). [9cd039b] Updated Homepage. [a36daf1] Rely on dpkg-dev for patching and removed build-dependancy on quilt. [51bde59] Support build-arch and build-indep targets through dh. [c3b9f16] Signal and configure the use of git-buildpackage. -- Charles Plessy Wed, 16 Nov 2011 14:37:03 +0900 clustalx (2.1+lgpl-1) unstable; urgency=low * New upstream archive, that makes clear the relicensing to LGPL-3+. - Mangled debian version name in debian/watch. - Explained why ‘+lgpl’ in debian/README.Debian. - Removed XS-Autobuild field from debian/control. - Changed archive area in debian/control. - Updated license in debian/copyright. - Removed Commercial field in debian/upstream-metadata.yaml. * Removed un-needed documentation (debian/clustalx.docs). * Source package hosted in a Git repository (debian/control). * Use debhelper 8 (debian/control, debian/compat). -- Charles Plessy Sun, 27 Feb 2011 22:36:51 +0900 clustalx (2.1-1) unstable; urgency=low * New upstream version * debian/rules: added get-upstream-changelog target and used it to obtain upstream changelog in debian/CHANGELOG.upstream -- Andreas Tille Wed, 24 Nov 2010 14:24:10 +0100 clustalx (2.0.12-3) unstable; urgency=low * debian/clustalx.desktop: Fixed typo Closes: #591613 * debian/control: - Added myself to uploaders - Standards-Version: 3.9.1 (no changes needed) * debian/source/format: 3.0 (quilt) -- Andreas Tille Wed, 04 Aug 2010 11:08:57 +0200 clustalx (2.0.12-2) unstable; urgency=low * Remove the moc_* files before building, to allow the use of later versions of Qt (debian/rules). * Incremented Standards-Version to reflect conformance with Policy 3.8.4 (debian/control, no other changes needed). -- Charles Plessy Fri, 29 Jan 2010 13:16:58 +0900 clustalx (2.0.12-1) unstable; urgency=low * New upstream release (LP: #423648, #393769): - Uses Qt instead of lesstif. - Includes new code for UPGMA guide trees. - Includes iterative alignment facility. [ Steffen Moeller ] * New upstream release. * Updated watch file (Closes: #550893). * Removed LICENSE from debian/clustalx.docs * rename to clustalx seems no longer required in debian/rules * moved clustalx.1 into debian folder (eases working with svn-buildpackage) * added German translation to desktop file [ Charles Plessy ] * Updated my email address. * debian/copyright made machine-readable. * Added various informations in debian/upstream-metadata.yaml. * Switched to Debhelper 7. (debian/rules, debian/control, debian/patches, debian/compat) * Removed useless Debhelper file debian/clustalx.dirs. * Updated package description. * Hardcoded the localisation of accessory files in /usr/share/clustalx. (debian/patches/hardcode-accessory-file-locations.patch) * Documented in debian/README.source that the documentation for quilt is in /usr/share/doc/quilt. * Added upstream changelog downloaded from upstream website (debian/rules, debian/CHANGELOG.upstream). * Incremented Standards-Version to reflect conformance with Policy 3.8.3 (debian/control, no other changes needed). * Updated homepage in debian/clustalw.1. -- Charles Plessy Wed, 21 Oct 2009 13:25:44 +0900 clustalx (1.83-4) unstable; urgency=low [ Charles Plessy ] * Transient package while Clustal X version > 2.0 is being relicenced. This package is the same as clustalw-1.83-3 except that it only builds the clustalx binary package (plus some minor improvements described in this changelog. In parallel, the Debian clustalw source package will stop building the clustalx binary package. * Association between Clustal X and .aln files: - text/x-clustalw-alignment associated to clustalx in clustalx.desktop. - .aln declared as text/x-clustalw-alignment in clustalx.sharedmimeinfo. - text/x-clustalw-alignment associated to clustalx in clustalx.mime. - debian/rules calls dh_installmime. * debian/control: - Allowed upload by Debian Maintainers. - Added Homepage: field. - Removed clustalw. - Checked conformance with Policy 3.7.3. [ Steffen Moeller ] * Updated watch file. * added German translation to desktop file -- Charles Plessy Thu, 21 Feb 2008 13:40:20 +0900 clustalw (1.83-3) unstable; urgency=low [ Nelson A. de Oliveira ] * Added watch file, debian/rules get-orig-source should be used to download the orig.tar.gz, not uscan. [ Charles Plessy ] * Build-depend on libncbi6-dev instead of ncbi-tools6-dev. [ Steffen Moeller ] * Added dependency to later version lesstif2 (Closes:#429480). * The recompilation against libvibrant6 was probably already fixed in an earlier version, certainly it is now (Closes:#378483). -- Charles Plessy Wed, 12 Sep 2007 16:50:37 +0900 clustalw (1.83-2) unstable; urgency=low [ Steffen Moeller ] * Help now works in ClustalX (Closes:#215414). * debian/control: - removed [biology] tag and improved debtags - better formatting/wording - suggesting alignment pretty-printers [ Charles Plessy ] * Add Subversion repository URL to debian/control. * FreeDesktop menu added (Closes: #380715) * Acknowledge NMU, thanks to Kai and Fabio. (Closes: #374241, #359712) * Collaborative maintainance: the maintainer is a mailing list, Steffen Moëller and Charles Plessy are uploaders. * Upgraded to debhelper 5. * Modified the copyright file to mention that it is not disallowed to use autobuilders to create binary packages. * Debian Menu transition: Apps/Science becomes Applications/Science/Biology. * Fixed a typo in clustalw.menu (Closes: #428518) * Updated Steffen's email adress. * Using quilt to manage the changes to the sources. -- Charles Plessy Sun, 12 Aug 2007 23:06:39 +0900 clustalw (1.83-1.2) unstable; urgency=high * Non-maintainer upload. * No changes, let's try to trigger again the builders. -- Fabio Tranchitella Fri, 10 Nov 2006 09:16:45 +0100 clustalw (1.83-1.1) unstable; urgency=low * Non-maintainer upload. * lesstif1 is deprecated, transition to lesstif2 (Closes: #374241) * Dead link in the package description (Closes: #359712) * Updated standards version, binary-indep rule required -- Kai Hendry Mon, 10 Jul 2006 11:04:05 +0900 clustalw (1.83-1) unstable; urgency=low * New upstream version * New maintainer * Reapplied patches from 1.82-3 * Removed calls to insecure gets * Cosmetics to makefile * Extension of description * Standards-Version: 3.5.10 * Increased version of debhelper: Build-Depends: debhelper (>= 4) * Used debian/compat for debhelper version * Replaces *.files by *.install, *.docs, *.manpages and used the apropriate tools in debian/rules * Moved clustalx to /usr/bin because it does not *belong* to the X11 system * Moved the manpage clustalx.1x to clustalx.1 accordingly. * Removed debian/dirs * Added menu entries -- Steffen Moeller Mon, 23 Jun 2003 19:26:29 +0100 clustalw (1.82-3) unstable; urgency=low * "My-wifes-Katrin-Birthday"-release (even if I doubt that she is very interested in Debian packaging details) * Fix a buffer override closes: #135255 -- Andreas Tille Wed, 27 Feb 2002 07:26:29 +0100 clustalw (1.82-2) unstable; urgency=low * also compile GUI clustalx which is included in the sources now -- Andreas Tille Sat, 3 Nov 2001 14:41:50 +0100 clustalw (1.82-1) unstable; urgency=low * New maintainer closes: #100213 * New upstream version closes: #40904 * Standards-Version: 3.5.6 * Moved help file to /usr/share/clustalw/clustalw_help because it is architecture independend * Added URL to the package description because I consider this as "good style" to have an upstream link without installing the package * Fixed a typo in the examples Makefile which was shiped with the Debian package: clustalw -profile -profile1=nuc.aln -profile2=nuc2.aln -outfile=profile.aln ^ this 2 was missing -- Andreas Tille Mon, 29 Oct 2001 21:40:20 +0100 clustalw (1.7-9) unstable; urgency=low * Maintainer set to Debian QA Group . -- Adrian Bunk Fri, 24 Aug 2001 21:09:56 +0200 clustalw (1.7-8) unstable; urgency=low * Adopted by new maintainer; closes: #92790 * Updated to latest standards version and added Build-Depends (changed makefile, control, dirs, docs, and rules); closes: #91132, #91411 * Deleted empty README.Debian file. * Corrected doc path in manpage. * Moved package to section non-free/science, because it is a tool that is exclusively useful for molecular biologists. -- Dr. Guenter Bechly Fri, 20 Apr 2001 19:08:00 +0200 clustalw (1.7-7) unstable; urgency=low * Better extended description. Closes #31475. * Manual page. Closes #31382. -- Stephane Bortzmeyer Wed, 31 Mar 1999 10:50:02 +0200 clustalw (1.7-6) unstable; urgency=low * Yet another attempt to get past rejection :-) Licence is now included in the copyright file. -- Stephane Bortzmeyer Sat, 19 Dec 1998 15:29:40 +0100 clustalw (1.7-5) unstable; urgency=low * A LICENCE is now included, non-free unfortunately. -- Stephane Bortzmeyer Thu, 17 Dec 1998 14:48:43 +0100 clustalw (1.7-4) unstable; urgency=low * Compiles with -mieee on the Alpha: otherwise, floating exception since ClustalW divides by zero (yuck!) -- Stephane Bortzmeyer Wed, 2 Dec 1998 16:16:02 +0100 clustalw (1.7-3) unstable; urgency=low * Tests and samples added * On line help file added -- Stephane Bortzmeyer Tue, 1 Dec 1998 15:57:50 +0100 clustalw (1.7-2) unstable; urgency=low * Switch to dh_make * First public release -- Stephane Bortzmeyer Tue, 1 Dec 1998 15:25:13 +0100 clustalw (1.7-1) unstable; urgency=low * Initial Release. -- Stephane Bortzmeyer Fri, 28 Aug 1998 16:09:48 +0200 debian/clustalx.install0000644000000000000000000000017111660647277012434 0ustar clustalx usr/bin clustalx.hlp usr/share/clustalx *xml usr/share/clustalx debian/clustalx.desktop usr/share/applications debian/clustalx.desktop0000644000000000000000000000155111660647277012442 0ustar [Desktop Entry] Version=1.0 Terminal=false Icon=clustalx Exec=clustalx Name=Clustal X GenericName=Alignment and phylogeny GenericName[de]=Alignment und Phylogenie GenericName[en]=Alignment and phylogeny GenericName[fr]=Alignement et phylogénèse GenericName[pt_BR]=Alinhamento e filogenia Comment=Global multiple nucleotide or peptide sequence alignment and phylogenetic analysis Comment[de]=Globales multiples Nucleotid- oder Peptid-Sequenzalignment and phylogenetische Analyse Comment[en]=Global multiple nucleotide or peptide sequence alignment and phylogenetic analysis Comment[fr]=Alignement global de séquences peptidiques ou nucléotidiques et analyse phylogénétique Comment[pt_BR]=Alinhamento global de sequências peptídicas ou nucleotídeos e análise filogenética Type=Application Categories=Biology;Science;Education; MimeType=text/x-clustalw-alignment; debian/copyright0000644000000000000000000000340211660647277011140 0ustar Format: http://dep.debian.net/deps/dep5/ Source: http://www.clustal.org/download/current/clustalx-2.1.tar.gz Files: * Copyright: © Des Higgins, Julie Thompson and Toby Gibson License: LGPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this program. If not, see . Comment: On Debian systems, you can read the full text of the GNU Lesser General Public License in ‘/usr/share/common-licenses/LGPL-3’. Files: debian/* Copyright: © 1998-1999 Stephane Bortzmeyer © 2001 Dr. Guenter Bechly © 2001 Adrian Bunk © 2001-2002 Andreas Tille © 2003-2008 Steffen Möller © 2006 Kai Hendry © 2007 Nelson A. de Oliveira © 2007–2011 Charles Plessy License: Unclear The licence of the earlier works was never stated. Some works have been obsoleted by release of version 2.0 — the lesstif migration for instance — but authors are left in the list of copyright holders by courtesy. The work of Charles Plessy and Steffen Möller can be treated as if it were public domain. debian/upstream-metadata.yaml0000644000000000000000000000127111660647277013511 0ustar Bugs: http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal Contact: clustalw@ucd.ie DOI: 10.1093/bioinformatics/btm404 Homepage: http://www.clustal.org/ PMID: 17846036 Reference: author: Larkin, M.A. and Blackshields, G. and Brown, N.P. and Chenna, R. and McGettigan, P.A. and McWilliam, H. and Valentin, F. and Wallace, I.M. and Wilm, A. and Lopez, R. and Thompson, J.D. and Gibson, T.J. and Higgins, D.G. title: Clustal W and Clustal X version 2.0 journal: Bioinformatics volume: 23 number: 21 pages: 2947-2948 year: 2007 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2947 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2947.pdf debian/clustalx.mime0000644000000000000000000000016211660647277011715 0ustar text/x-clustalw-alignment; clustalx '%s'; description=Clustal W multiple sequence alignment; nametemplate=%s.aln debian/clustalx.manpages0000644000000000000000000000002211660647277012554 0ustar debian/clustalx.1 debian/gbp.conf0000644000000000000000000000032011660647277010620 0ustar # This source package is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/README.Debian0000644000000000000000000000063211660647277011250 0ustar Clustal X for Debian ──────────────────── Since version 2.1, Clustal is free software. The upstream archives have been updated in December 2010 to clarify that, but their version number was not changed. Because the Debian archive does not support this, the Debian package's version is 2.1+lgpl. -- Charles Plessy Sun, 27 Feb 2011 19:39:17 +0900 debian/clustalx.10000644000000000000000000000302611660647277011130 0ustar .TH CLUSTALW 1 "2003 July 1" "Manual for clustalw" .SH NAME clustalw \- a multiple sequence alignment program .SH SYNOPSIS .B clustalw .I "[options]" .SH "DESCRIPTION" This manual page documents briefly the .BR clustalx command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has other documentation; see below. .PP .B clustalx is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. .P You can cut-and-paste sequences to change the order of the alignment; you can select a subset of sequences to be aligned; you can select a sub-range of the alignment to be realigned and inserted back into the original alignment. .P Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. .SH "SEE ALSO" Files in /usr/share/doc/clustalx contain a lot of details. The Web page is also helpful. .SH AUTHOR This manual page was written by Andreas Tille , for the Debian GNU/Linux system (but may be used by others). debian/patches/0000755000000000000000000000000011660647277010635 5ustar debian/patches/hardcode-accessory-file-locations.patch0000644000000000000000000000262311660647277020331 0ustar Author: Charles Plessy Forwarded: ClustalW Description: Hardcodes the location of help and color files to /usr/share/clustalx. When not patched, Clustal X will search for this files in the same directory as where the binary program is, but in Debian we do not distribute data in /usr/bin. . Alternatively, we could ship the XML files in /etc/clustal and treat them as configuration files. Please notify the Debian Med team if you think it is necessary. --- clustalx-2.0.12.orig/ClustalQtParams.h +++ clustalx-2.0.12/ClustalQtParams.h @@ -13,9 +13,9 @@ #include "clustalW/alignment/Alignment.h" #include -static QString psColorFile = "colprot.xml"; -static QString psDNAFile = "coldna.xml"; -static QString psPrintFile = "colprint.xml"; +static QString psColorFile = "/usr/share/clustalx/colprot.xml"; +static QString psDNAFile = "/usr/share/clustalx/coldna.xml"; +static QString psPrintFile = "/usr/share/clustalx/colprint.xml"; static const int BlackAndWhite = 1; static const int ColorsBackGround = 2; --- clustalx-2.0.12.orig/HelpDisplayWidget.cpp +++ clustalx-2.0.12/HelpDisplayWidget.cpp @@ -19,7 +19,7 @@ #include #include "Resources.h" -const string HelpDisplayWidget::helpFileName = "clustalx.hlp"; +const string HelpDisplayWidget::helpFileName = "/usr/share/clustalx/clustalx.hlp"; HelpDisplayWidget::HelpDisplayWidget(char helpPointer) { debian/patches/series0000644000000000000000000000005011660647277012045 0ustar hardcode-accessory-file-locations.patch debian/rules0000755000000000000000000000050411660647277010265 0ustar #!/usr/bin/make -f %: dh $@ override_dh_auto_configure: qmake-qt4 override_dh_clean: $(RM) moc_* dh_clean override_dh_installchangelogs: dh_installchangelogs debian/CHANGELOG.upstream get-upstream-changelog: cd debian; wget -N --output-document=CHANGELOG.upstream http://www.clustal.org/download/current/CHANGELOG debian/clustalx.menu0000644000000000000000000000024311660647277011732 0ustar ?package(clustalx):needs="X11" \ section="Applications/Science/Biology" \ title="ClustalX" \ command="/usr/bin/clustalx"\ hints="GUI for clustalw" debian/source/0000755000000000000000000000000011660647277010506 5ustar debian/source/format0000644000000000000000000000001411660647277011714 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000211660647277010404 0ustar 8