[med-svn] r1641 - trunk/packages/clustalw/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Thu Mar 20 10:54:52 UTC 2008
Author: charles-guest
Date: 2008-03-20 10:54:51 +0000 (Thu, 20 Mar 2008)
New Revision: 1641
Added:
trunk/packages/clustalw/trunk/debian/clustalw.1.xml
Modified:
trunk/packages/clustalw/trunk/debian/changelog
trunk/packages/clustalw/trunk/debian/clustalw.1
Log:
Added a manpage, that I will submit in Upstrams bugzilla
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-03-20 07:03:44 UTC (rev 1640)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-03-20 10:54:51 UTC (rev 1641)
@@ -5,8 +5,10 @@
Added a X-Non-Free-Autobuild field to fullfill requirements from
http://lists.debian.org/msgid-search/20061129152824.GT2560@mails.so.argh.org
* Updated CHANGELOG from http://www.clustal.org/download/current/CHANGELOG
+ * debian/clustalw.1.xml, rewritten from scratch.
+ * debian/clustalw.q: updated from the DocBook sources (Closes: #463591).
- -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 19 Mar 2008 13:15:20 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 20 Mar 2008 15:42:38 +0900
clustalw (2.0.4-1) unstable; urgency=low
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1 2008-03-20 07:03:44 UTC (rev 1640)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1 2008-03-20 10:54:51 UTC (rev 1641)
@@ -1,56 +1,648 @@
-.TH CLUSTALW 1
-.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
-.\" other parms are allowed: see man(7), man(1)
-.SH NAME
-clustalw \- a multiple sequence alignment program
-
-.SH SYNOPSIS
-.B clustalw
-.I "[options]"
+.\" Title: CLUSTALW
+.\" Author: Des Higgins
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 03/20/2008
+.\" Manual: Clustal Manual
+.\" Source: Clustal 2.0.5
+.\"
+.TH "CLUSTALW" "1" "03/20/2008" "Clustal 2.0.5" "Clustal Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+clustalw - Multiple alignment of nucleic acid and protein sequences
+.SH "SYNOPSIS"
+.HP 9
+\fBclustalw\fR [\fB\-infile\fR] \fIfile\.ext\fR [\fBOPTIONS\fR]
+.HP 9
+\fBclustalw\fR [\fB\-help\fR | \fB\-fullhelp\fR]
.SH "DESCRIPTION"
-This manual page documents briefly the
-.BR clustalw
-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 clustalw
-is a program which performs
-simultaneous alignment of many nucleotide or amino acid sequences.
-It is typically run interactively, providing a menu and an online help.
-If you prefer to use it in command-line (batch) mode, you will have
-to give several options, the minimum being \-infile.
-.SH OPTIONS
-A summary of options are included below.
-For a complete description, see the last section.
-.TP
-.B \-infile=string
-Tells ClustalW to get input from the named file.
-Several formats are automatically recognized.
-.TP
-.B \-outfile=string
-Tells ClustalW to write output in the named file.
-.TP
-.B \-tree
-Calculates NJ tree.
-.TP
-.B \-profile
-Merges two alignments by profile alignment.
-.TP
-.B \-output=string
-Sets the output format. It can be GCG, GDE, PHYLIP or PIR.
-.TP
-.B \-quicktree
-Uses FAST algorithm for the alignment guide tree.
-.TP
-.B \-help
-Prints a short help. Warning: the syntax of the options is the VMS one. For
-Unix, change the / to a - and type the option name in lower case.
+Clustal\ W is a general purpose multiple alignment program for DNA or proteins\.
+.SH "OPTIONS"
+.SS "DATA (sequences)"
+.PP
+\fB \-infile=\fR\fB\fIfile\.ext\fR\fR\fB \fR
+.RS 4
+Input sequences\.
+.RE
+.PP
+\fB \-profile1=\fR\fB\fIfile\.ext\fR\fR\fB and \-profile2=\fR\fB\fIfile\.ext\fR\fR\fB \fR
+.RS 4
+Profiles (old alignment)
+.RE
+.SS "VERBS (do things)"
+.PP
+\fB\-options\fR
+.RS 4
+List the command line parameters\.
+.RE
+.PP
+\fB\-help or \-check\fR
+.RS 4
+Outline the command line params\.
+.RE
+.PP
+\fB\-fullhelp\fR
+.RS 4
+Dump the built\-in help file content\.
+.RE
+.PP
+\fB\-align\fR
+.RS 4
+Do full multiple alignment\.
+.RE
+.PP
+\fB\-tree\fR
+.RS 4
+Calculate NJ tree\.
+.RE
+.PP
+\fB \-bootstrap\fR\fB\fI=n\fR\fR\fB \fR
+.RS 4
+Bootstrap a NJ tree (\fIn\fR= number of bootstraps; def\. = 1000)\.
+.RE
+.PP
+\fB\-convert\fR
+.RS 4
+Output the input sequences in a different file format\.
+.RE
+.SS "PARAMETERS (set things)"
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+General settings:
+.RS
+.PP
+\fB\-interactive\fR
+.RS 4
+Read command line, then enter normal interactive menus\.
+.RE
+.PP
+\fB\-quicktree\fR
+.RS 4
+Use FAST algorithm for the alignment guide tree\.
+.RE
+.PP
+\fB\-type=\fR
+.RS 4
+\fIPROTEIN\fR
+or
+\fIDNA\fR
+sequences\.
+.RE
+.PP
+\fB\-negative\fR
+.RS 4
+Protein alignment with negative values in matrix\.
+.RE
+.PP
+\fB\-outfile=\fR
+.RS 4
+Sequence alignment file name\.
+.RE
+.PP
+\fB\-output=\fR
+.RS 4
+\fIGCG\fR,
+\fIGDE\fR,
+\fIPHYLIP\fR,
+\fIPIR\fR
+or
+\fINEXUS\fR\.
+.RE
+.PP
+\fB\-outputorder=\fR
+.RS 4
+\fIINPUT\fR
+or
+\fIALIGNED\fR
+.RE
+.PP
+\fB\-case\fR
+.RS 4
+\fILOWER\fR
+or
+\fIUPPER\fR
+(for GDE output only)\.
+.RE
+.PP
+\fB\-seqnos=\fR
+.RS 4
+\fIOFF\fR
+or
+\fION\fR
+(for Clustal output only)\.
+.RE
+.PP
+\fB\-seqnos_range=\fR
+.RS 4
+\fIOFF\fR
+or
+\fION\fR
+(NEW: for all output formats)\.
+.RE
+.PP
+\fB\-range=\fR\fB\fIm\fR\fR\fB,\fR\fB\fIn\fR\fR
+.RS 4
+Sequence range to write starting
+\fIm\fR
+to
+\fIm\fR+\fIn\fR\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Fast Pairwise Alignments:
+.RS
+.PP
+\fB\-ktuple=\fR\fB\fIn\fR\fR
+.RS 4
+Word size\.
+.RE
+.PP
+\fB\-topdiags=\fR\fB\fIn\fR\fR
+.RS 4
+Number of best diags\.
+.RE
+.PP
+\fB\-window=\fR\fB\fIn\fR\fR
+.RS 4
+Window around best diags\.
+.RE
+.PP
+\fB\-pairgap=\fR\fB\fIn\fR\fR
+.RS 4
+Gap penalty\.
+.RE
+.PP
+\fB\-score\fR
+.RS 4
+\fIPERCENT\fR
+or
+\fIABSOLUTE\fR\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Slow Pairwise Alignments:
+.RS
+.PP
+\fB\-pwmatrix=\fR
+.RS 4
+:Protein weight matrix=\fIBLOSUM\fR,
+\fIPAM\fR,
+\fIGONNET\fR,
+\fIID\fR
+or
+\fIfilename\fR
+.RE
+.PP
+\fB\-pwdnamatrix=\fR
+.RS 4
+DNA weight matrix=\fIBLOSUM\fRIUB,
+\fIBLOSUM\fRCLUSTALW or
+\fIBLOSUM\fRfilename\.
+.RE
+.PP
+\fB\-pwgapopen=\fR\fB\fIf\fR\fR
+.RS 4
+Gap opening penalty\.
+.RE
+.PP
+\fB\-pwgapext=\fR\fB\fIf\fR\fR
+.RS 4
+Gap extension penalty\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Multiple Alignments:
+.RS
+.PP
+\fB\-newtree=\fR
+.RS 4
+File for new guide tree\.
+.RE
+.PP
+\fB\-usetree=\fR
+.RS 4
+File for old guide tree\.
+.RE
+.PP
+\fB\-matrix=\fR
+.RS 4
+Protein weight matrix=\fIBLOSUM\fR,
+\fIPAM\fR,
+\fIGONNET\fR,
+\fIID\fR
+or
+\fIfilename\fR\.
+.RE
+.PP
+\fB\-dnamatrix=\fR
+.RS 4
+DNA weight matrix=\fIIUB\fR,
+\fICLUSTALW\fR
+or
+\fIfilename\fR\.
+.RE
+.PP
+\fB\-gapopen=\fR\fB\fIf\fR\fR
+.RS 4
+Gap opening penalty\.
+.RE
+.PP
+\fB\-gapext=\fR\fB\fIf\fR\fR
+.RS 4
+Gap extension penalty\.
+.RE
+.PP
+\fB\-engaps\fR
+.RS 4
+No end gap separation pen\.
+.RE
+.PP
+\fB\-gapdist=\fR\fB\fIn\fR\fR
+.RS 4
+Gap separation pen\. range\.
+.RE
+.PP
+\fB\-nogap\fR
+.RS 4
+Residue\-specific gaps off\.
+.RE
+.PP
+\fB\-nohgap\fR
+.RS 4
+Hydrophilic gaps off\.
+.RE
+.PP
+\fB\-hgapresidues=\fR
+.RS 4
+List hydrophilic res\.
+.RE
+.PP
+\fB\-maxdiv=\fR\fB\fIn\fR\fR
+.RS 4
+Percent identity for delay\.
+.RE
+.PP
+\fB\-type=\fR
+.RS 4
+\fIPROTEIN\fR
+or
+\fIDNA\fR
+.RE
+.PP
+\fB\-transweight=\fR\fB\fIf\fR\fR
+.RS 4
+Transitions weighting\.
+.RE
+.PP
+\fB\-iteration=\fR
+.RS 4
+\fINONE\fR
+or
+\fITREE\fR
+or
+\fIALIGNMENT\fR\.
+.RE
+.PP
+\fB\-numiter=\fR\fB\fIn\fR\fR
+.RS 4
+Maximum number of iterations to perform\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Profile Alignments:
+.RS
+.PP
+\fB\-profile\fR
+.RS 4
+Merge two alignments by profile alignment\.
+.RE
+.PP
+\fB\-newtree1=\fR
+.RS 4
+File for new guide tree for profile1\.
+.RE
+.PP
+\fB\-newtree2=\fR
+.RS 4
+File for new guide tree for profile2\.
+.RE
+.PP
+\fB\-usetree1=\fR
+.RS 4
+File for old guide tree for profile1\.
+.RE
+.PP
+\fB\-usetree2=\fR
+.RS 4
+File for old guide tree for profile2\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Sequence to Profile Alignments:
+.RS
+.PP
+\fB\-sequences\fR
+.RS 4
+Sequentially add profile2 sequences to profile1 alignment\.
+.RE
+.PP
+\fB\-newtree=\fR
+.RS 4
+File for new guide tree\.
+.RE
+.PP
+\fB\-usetree=\fR
+.RS 4
+File for old guide tree\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Structure Alignments:
+.RS
+.PP
+\fB\-nosecstr1\fR
+.RS 4
+Do not use secondary structure\-gap penalty mask for profile 1\.
+.RE
+.PP
+\fB\-nosecstr2\fR
+.RS 4
+Do not use secondary structure\-gap penalty mask for profile 2\.
+.RE
+.PP
+\fB\-secstrout=\fR\fB\fISTRUCTURE\fR\fR\fB or \fR\fB\fIMASK\fR\fR\fB or \fR\fB\fIBOTH\fR\fR\fB or \fR\fB\fINONE\fR\fR
+.RS 4
+Output in alignment file\.
+.RE
+.PP
+\fB\-helixgap=\fR\fB\fIn\fR\fR
+.RS 4
+Gap penalty for helix core residues\.
+.RE
+.PP
+\fB\-strandgap=\fR\fB\fIn\fR\fR
+.RS 4
+Gap penalty for strand core residues\.
+.RE
+.PP
+\fBloopgap=\fR\fB\fIn\fR\fR
+.RS 4
+Gap penalty for loop regions\.
+.RE
+.PP
+\fB\-terminalgap=\fR\fB\fIn\fR\fR
+.RS 4
+Gap penalty for structure termini\.
+.RE
+.PP
+\fB\-helixendin=\fR\fB\fIn\fR\fR
+.RS 4
+Number of residues inside helix to be treated as terminal\.
+.RE
+.PP
+\fB\-helixendout=\fR\fB\fIn\fR\fR
+.RS 4
+Number of residues outside helix to be treated as terminal\.
+.RE
+.PP
+\fB\-strandendin=\fR\fB\fIn\fR\fR
+.RS 4
+Number of residues inside strand to be treated as terminal\.
+.RE
+.PP
+\fB\-strandendout=\fR\fB\fIn\fR\fR
+.RS 4
+Number of residues outside strand to be treated as terminal\.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Trees:
+.RS
+.PP
+\fB\-outputtree=\fR\fB\fInj\fR\fR\fB OR \fR\fB\fIphylip\fR\fR\fB OR \fR\fB\fIdist\fR\fR\fB OR \fR\fB\fInexus\fR\fR
+.RS 4
+.RE
+.PP
+\fB\-seed=\fR\fB\fIn\fR\fR
+.RS 4
+Seed number for bootstraps\.
+.RE
+.PP
+\fB\-kimura\fR
+.RS 4
+Use Kimura\'s correction\.
+.RE
+.PP
+\fB\-tossgaps\fR
+.RS 4
+Ignore positions with gaps\.
+.RE
+.PP
+\fB\-bootlabels=\fR\fB\fInode\fR\fR
+.RS 4
+Position of bootstrap values in tree display\.
+.RE
+.PP
+\fB\-clustering=\fR
+.RS 4
+NJ or UPGMA\.
+.RE
+.RE
+.SH "BUGS"
+.PP
+The Clustal bug tracking system can be found at
+\fI\%http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal\fR\.
.SH "SEE ALSO"
-The \-help option is a good summary. Files in /usr/share/doc/clustalw contains a lot
-of details. The Web page <http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/>
-is also helpful.
-.SH AUTHOR
-This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
-for the Debian GNU/Linux system (but may be used by others).
+.PP
+\fBclustalx\fR(1)\.
+.SH "REFERENCES"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG\. (2007)\.
+\fIClustal W and Clustal X version 2\.0\.\fR\&[1]
+Bioinformatics, 23, 2947\-2948\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD\. (2003)\.
+\fIMultiple sequence alignment with the Clustal series of programs\.\fR\&[2]
+Nucleic Acids Res\., 31, 3497\-3500\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ\. (1998)\.
+\fIMultiple sequence alignment with Clustal X\fR\&[3]\. Trends Biochem Sci\., 23, 403\-405\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG\. (1997)\.
+\fIThe CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools\.\fR\&[4]
+Nucleic Acids Res\., 25, 4876\-4882\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Higgins DG, Thompson JD, Gibson TJ\. (1996)\.
+\fIUsing CLUSTAL for multiple sequence alignments\.\fR\&[5]
+Methods Enzymol\., 266, 383\-402\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Thompson JD, Higgins DG, Gibson TJ\. (1994)\.
+\fICLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position\-specific gap penalties and weight matrix choice\.\fR\&[6]
+Nucleic Acids Res\., 22, 4673\-4680\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Higgins DG\. (1994)\.
+\fICLUSTAL V: multiple alignment of DNA and protein sequences\.\fR\&[7]
+Methods Mol Biol\., 25, 307\-318
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Higgins DG, Bleasby AJ, Fuchs R\. (1992)\.
+\fICLUSTAL V: improved software for multiple sequence alignment\.\fR\&[8]
+Comput\. Appl\. Biosci\., 8, 189\-191\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Higgins,D\.G\. and Sharp,P\.M\. (1989)\.
+\fIFast and sensitive multiple sequence alignments on a microcomputer\.\fR\&[9]
+Comput\. Appl\. Biosci\., 5, 151\-153\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Higgins,D\.G\. and Sharp,P\.M\. (1988)\.
+\fICLUSTAL: a package for performing multiple sequence alignment on a microcomputer\.\fR\&[10]
+Gene, 73, 237\-244\.
+.RE
+.SH "AUTHORS"
+.PP
+\fBDes Higgins\fR
+.sp -1n
+.IP "" 4
+Copyright holder for Clustal\.
+.PP
+\fBJulie Thompson\fR
+.sp -1n
+.IP "" 4
+Copyright holder for Clustal\.
+.PP
+\fBToby Gibson\fR
+.sp -1n
+.IP "" 4
+Copyright holder for Clustal\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Prepared this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+Copyright \(co 1988\(en2008 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
+.br
+Copyright \(co 2008 Charles Plessy (This manpage)
+.br
+.PP
+The binaries and source code are made available and can be distributed subject to the following conditions:
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Users are free to redistribute Clustal\ W or Clustal\ X in it\'s unmodified form as long as it is not for commercial gain\.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at
+<gibson at embl\.de>
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at
+<clustalw at ucd\.ie>
+where they will be considered for inclusion in future releases\.
+.RE
+.PP
+This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\.
+.sp
+.SH "NOTES"
+.IP " 1." 4
+Clustal W and Clustal X version 2.0.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/17846036
+.RE
+.IP " 2." 4
+Multiple sequence alignment with the Clustal series of programs.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/12824352
+.RE
+.IP " 3." 4
+Multiple sequence alignment with Clustal X
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/9810230
+.RE
+.IP " 4." 4
+The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/9396791
+.RE
+.IP " 5." 4
+Using CLUSTAL for multiple sequence alignments.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/8743695
+.RE
+.IP " 6." 4
+CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/7984417
+.RE
+.IP " 7." 4
+CLUSTAL V: multiple alignment of DNA and protein sequences.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/8004173
+.RE
+.IP " 8." 4
+CLUSTAL V: improved software for multiple sequence alignment.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/1591615
+.RE
+.IP " 9." 4
+Fast and sensitive multiple sequence alignments on a microcomputer.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/2720464
+.RE
+.IP "10." 4
+CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
+.RS 4
+\%http://www.ncbi.nlm.nih.gov/pubmed/3243435
+.RE
Added: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml (rev 0)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-03-20 10:54:51 UTC (rev 1641)
@@ -0,0 +1,905 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Template from docbook-xsl-1.73.2.dfsg.1-3 -->
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "2.0.5">
+ <!ENTITY dhtitle "Clustal Manual">
+ <!ENTITY dhucpackage "CLUSTALW">
+ <!ENTITY dhpackage "clustalw">
+ <!ENTITY dhproduct "Clustal">
+ <!ENTITY dhsection "1">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Des</firstname>
+ <surname>Higgins</surname>
+ <contrib>Copyright holder for &dhproduct;.</contrib>
+ </author>
+ <author>
+ <firstname>Julie</firstname>
+ <surname>Thompson</surname>
+ <contrib>Copyright holder for &dhproduct;.</contrib>
+ </author>
+ <author>
+ <firstname>Toby</firstname>
+ <surname>Gibson</surname>
+ <contrib>Copyright holder for &dhproduct;.</contrib>
+ </author>
+ </authorgroup>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Prepared this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <!-- I am unsure of the years, please correct me if I am wrong ! Charles -->
+ <year>1988–2008</year>
+ <holder>Des Higgins, Julie Thompson & Toby Giboson (&dhproduct;)</holder>
+ </copyright>
+ <copyright>
+ <year>2008</year>
+ <holder>&dhusername; (This manpage)</holder>
+ </copyright>
+ <legalnotice>
+ <para>
+ The binaries and source code are made available and can be distributed subject to the following conditions:
+ </para>
+ <itemizedlist>
+ <listitem>
+ <para>
+ Users are free to redistribute Clustal W or Clustal X in it's unmodified form as long as it is not for commercial gain.
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at <email>gibson at embl.de</email>
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at <email>clustalw at ucd.ie</email> where they will be considered for inclusion in future releases.
+ </para>
+ </listitem>
+ </itemizedlist>
+ </legalnotice>
+ <legalnotice>
+ <para>
+ This manual page and its XML source can be used, modified, and redistributed as if it were in public domain.
+ </para>
+ </legalnotice>
+ </refentryinfo>
+
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Multiple alignment of nucleic acid and protein sequences</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>-infile</option></arg>
+ <arg choice="plain"><replaceable>file.ext</replaceable></arg>
+ <arg choice="opt"><option>OPTIONS</option></arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- Normally the help and version options make the programs stop
+ right after outputting the requested information. -->
+ <group choice="opt">
+ <arg choice="plain"><option>-help</option></arg>
+ <arg choice="plain"><option>-fullhelp</option></arg>
+ </group>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>Clustal W is a general purpose multiple alignment program for DNA or proteins.</para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <refsect2 id="data">
+ <title>DATA (sequences)</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term>
+ <option>
+ -infile=<replaceable class="parameter">file.ext</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>Input sequences.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>
+ -profile1=<replaceable class="parameter">file.ext</replaceable> and -profile2=<replaceable class="parameter">file.ext</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>Profiles (old alignment)</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect2>
+
+ <refsect2 id="verbs">
+ <title>VERBS (do things)</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-options</option>
+ </term>
+ <listitem>
+ <para>List the command line parameters.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-help or -check</option>
+ </term>
+ <listitem>
+ <para>Outline the command line params.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-fullhelp</option>
+ </term>
+ <listitem>
+ <para>Dump the built-in help file content.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-align</option>
+ </term>
+ <listitem>
+ <para>Do full multiple alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-tree</option>
+ </term>
+ <listitem>
+ <para>Calculate NJ tree.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>
+ -bootstrap<replaceable class="parameter">=n</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>Bootstrap a NJ tree (<replaceable class="parameter">n</replaceable>= number of bootstraps; def. = 1000).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-convert</option>
+ </term>
+ <listitem>
+ <para>Output the input sequences in a different file format.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect2>
+
+ <refsect2 id="parameters">
+ <title>PARAMETERS (set things)</title>
+ <refsect3 id="general-settings">
+ <title>General settings:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-interactive</option>
+ </term>
+ <listitem>
+ <para>Read command line, then enter normal interactive menus.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-quicktree</option>
+ </term>
+ <listitem>
+ <para>Use FAST algorithm for the alignment guide tree.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-type=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">PROTEIN</replaceable> or <replaceable class="parameter">DNA</replaceable> sequences.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-negative</option>
+ </term>
+ <listitem>
+ <para>Protein alignment with negative values in matrix.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-outfile=</option>
+ </term>
+ <listitem>
+ <para>Sequence alignment file name.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-output=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">GCG</replaceable>, <replaceable class="parameter">GDE</replaceable>, <replaceable class="parameter">PHYLIP</replaceable>, <replaceable class="parameter">PIR</replaceable> or <replaceable class="parameter">NEXUS</replaceable>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-outputorder=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">INPUT</replaceable> or <replaceable class="parameter">ALIGNED</replaceable></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-case</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">LOWER</replaceable> or <replaceable class="parameter">UPPER</replaceable> (for GDE output only).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-seqnos=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">OFF</replaceable> or <replaceable class="parameter">ON</replaceable> (for Clustal output only).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-seqnos_range=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">OFF</replaceable> or <replaceable class="parameter">ON</replaceable> (NEW: for all output formats).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-range=<replaceable class="parameter">m</replaceable>,<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Sequence range to write starting <replaceable class="parameter">m</replaceable> to <replaceable class="parameter">m</replaceable>+<replaceable class="parameter">n</replaceable>.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 id="fast">
+ <title>Fast Pairwise Alignments:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-ktuple=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Word size.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-topdiags=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Number of best diags.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-window=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Window around best diags.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-pairgap=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap penalty.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-score</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">PERCENT</replaceable> or <replaceable class="parameter">ABSOLUTE</replaceable>.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 id="slow">
+ <title>Slow Pairwise Alignments:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-pwmatrix=</option>
+ </term>
+ <listitem>
+ <para>:Protein weight matrix=<replaceable class="parameter">BLOSUM</replaceable>, <replaceable class="parameter">PAM</replaceable>, <replaceable class="parameter">GONNET</replaceable>, <replaceable class="parameter">ID</replaceable> or <replaceable class="parameter">filename</replaceable></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-pwdnamatrix=</option>
+ </term>
+ <listitem>
+ <para>DNA weight matrix=<replaceable class="parameter">BLOSUM</replaceable>IUB, <replaceable class="parameter">BLOSUM</replaceable>CLUSTALW or <replaceable class="parameter">BLOSUM</replaceable>filename.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-pwgapopen=<replaceable class="parameter">f</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap opening penalty.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-pwgapext=<replaceable class="parameter">f</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap extension penalty.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 lang="multiple">
+ <title>Multiple Alignments:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-newtree=</option>
+ </term>
+ <listitem>
+ <para>File for new guide tree.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-usetree=</option>
+ </term>
+ <listitem>
+ <para>File for old guide tree.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-matrix=</option>
+ </term>
+ <listitem>
+ <para>Protein weight matrix=<replaceable class="parameter">BLOSUM</replaceable>, <replaceable class="parameter">PAM</replaceable>, <replaceable class="parameter">GONNET</replaceable>, <replaceable class="parameter">ID</replaceable> or <replaceable class="parameter">filename</replaceable>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-dnamatrix=</option>
+ </term>
+ <listitem>
+ <para>DNA weight matrix=<replaceable class="parameter">IUB</replaceable>, <replaceable class="parameter">CLUSTALW</replaceable> or <replaceable class="parameter">filename</replaceable>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-gapopen=<replaceable class="parameter">f</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap opening penalty.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-gapext=<replaceable class="parameter">f</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap extension penalty.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-engaps</option>
+ </term>
+ <listitem>
+ <para>No end gap separation pen.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-gapdist=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap separation pen. range.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-nogap</option>
+ </term>
+ <listitem>
+ <para>Residue-specific gaps off.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-nohgap</option>
+ </term>
+ <listitem>
+ <para>Hydrophilic gaps off.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-hgapresidues=</option>
+ </term>
+ <listitem>
+ <para>List hydrophilic res.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-maxdiv=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Percent identity for delay.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-type=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">PROTEIN</replaceable> or <replaceable class="parameter">DNA</replaceable></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-transweight=<replaceable class="parameter">f</replaceable></option>
+ </term>
+ <listitem>
+ <para>Transitions weighting.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-iteration=</option>
+ </term>
+ <listitem>
+ <para><replaceable class="parameter">NONE</replaceable> or <replaceable class="parameter">TREE</replaceable> or <replaceable class="parameter">ALIGNMENT</replaceable>.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-numiter=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Maximum number of iterations to perform.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 id="profile">
+ <title>Profile Alignments:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-profile</option>
+ </term>
+ <listitem>
+ <para>Merge two alignments by profile alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-newtree1=</option>
+ </term>
+ <listitem>
+ <para>File for new guide tree for profile1.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-newtree2=</option>
+ </term>
+ <listitem>
+ <para>File for new guide tree for profile2.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-usetree1=</option>
+ </term>
+ <listitem>
+ <para>File for old guide tree for profile1.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-usetree2=</option>
+ </term>
+ <listitem>
+ <para>File for old guide tree for profile2.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 id="seq-to-profile">
+ <title>Sequence to Profile Alignments:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-sequences</option>
+ </term>
+ <listitem>
+ <para>Sequentially add profile2 sequences to profile1 alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-newtree=</option>
+ </term>
+ <listitem>
+ <para>File for new guide tree.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-usetree=</option>
+ </term>
+ <listitem>
+ <para>File for old guide tree.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 id="structure">
+ <title>Structure Alignments:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-nosecstr1</option>
+ </term>
+ <listitem>
+ <para>Do not use secondary structure-gap penalty mask for profile 1.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-nosecstr2</option>
+ </term>
+ <listitem>
+ <para>Do not use secondary structure-gap penalty mask for profile 2.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-secstrout=<replaceable class="parameter">STRUCTURE</replaceable> or <replaceable class="parameter">MASK</replaceable> or <replaceable class="parameter">BOTH</replaceable> or <replaceable class="parameter">NONE</replaceable></option>
+ </term>
+ <listitem>
+ <para>Output in alignment file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-helixgap=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap penalty for helix core residues.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-strandgap=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap penalty for strand core residues.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>loopgap=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap penalty for loop regions.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-terminalgap=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Gap penalty for structure termini.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-helixendin=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Number of residues inside helix to be treated as terminal.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-helixendout=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Number of residues outside helix to be treated as terminal.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-strandendin=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Number of residues inside strand to be treated as terminal.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-strandendout=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Number of residues outside strand to be treated as terminal.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+
+ <refsect3 id="trees">
+ <title>Trees:</title>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-outputtree=<replaceable class="parameter">nj</replaceable> OR <replaceable class="parameter">phylip</replaceable> OR <replaceable class="parameter">dist</replaceable> OR <replaceable class="parameter">nexus</replaceable></option>
+ </term>
+ <listitem>
+ <para></para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-seed=<replaceable class="parameter">n</replaceable></option>
+ </term>
+ <listitem>
+ <para>Seed number for bootstraps.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-kimura</option>
+ </term>
+ <listitem>
+ <para>Use Kimura's correction.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-tossgaps</option>
+ </term>
+ <listitem>
+ <para>Ignore positions with gaps.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-bootlabels=<replaceable class="parameter">node</replaceable></option>
+ </term>
+ <listitem>
+ <para>Position of bootstrap values in tree display.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-clustering=</option>
+ </term>
+ <listitem>
+ <para>NJ or UPGMA.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect3>
+ </refsect2>
+ </refsect1>
+
+ <refsect1 id="bugs">
+ <!-- Or use this section to tell about upstream BTS. -->
+ <title>BUGS</title>
+ <para>The &dhproduct; bug tracking system can be found at <ulink url="http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal"/>.</para>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>clustalx</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>.</para>
+ </refsect1>
+
+ <refsect1 id="references">
+ <title>REFERENCES</title>
+ <itemizedlist>
+ <listitem>
+ <para>
+ Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/17846036">Clustal W and Clustal X version 2.0.</ulink> Bioinformatics, 23, 2947-2948.
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/12824352">Multiple sequence alignment with the Clustal series of programs.</ulink> Nucleic Acids Res., 31, 3497-3500.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. (1998). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/9810230">Multiple sequence alignment with Clustal X</ulink>. Trends Biochem Sci., 23, 403-405.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/9396791">The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.</ulink> Nucleic Acids Res., 25, 4876-4882.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Higgins DG, Thompson JD, Gibson TJ. (1996). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/8743695">Using CLUSTAL for multiple sequence alignments.</ulink> Methods Enzymol., 266, 383-402.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Thompson JD, Higgins DG, Gibson TJ. (1994). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/7984417">CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.</ulink> Nucleic Acids Res., 22, 4673-4680.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Higgins DG. (1994). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/8004173">CLUSTAL V: multiple alignment of DNA and protein sequences.</ulink> Methods Mol Biol., 25, 307-318
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Higgins DG, Bleasby AJ, Fuchs R. (1992). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/1591615">CLUSTAL V: improved software for multiple sequence alignment.</ulink> Comput. Appl. Biosci., 8, 189-191.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Higgins,D.G. and Sharp,P.M. (1989). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/2720464">Fast and sensitive multiple sequence alignments on a microcomputer.</ulink> Comput. Appl. Biosci., 5, 151-153.
+ </para>
+ </listitem>
+
+ <listitem>
+ <para>
+ Higgins,D.G. and Sharp,P.M. (1988). <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/3243435">CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.</ulink> Gene, 73, 237-244.
+ </para>
+ </listitem>
+ </itemizedlist>
+ </refsect1>
+</refentry>
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