'\" t
.\"     Title: CLUSTALW
.\"    Author: Des Higgins
.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
.\"      Date: 12/28/2010
.\"    Manual: Clustal Manual
.\"    Source: Clustal 2.1
.\"  Language: English
.\"
.TH "CLUSTALW" "1" "12/28/2010" "Clustal 2.1" "Clustal Manual"
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.SH "NAME"
clustalw \- Multiple alignment of nucleic acid and protein sequences
.SH "SYNOPSIS"
.HP \w'\fBclustalw\fR\ 'u
\fBclustalw\fR [\fB\-infile\fR] \fIfile\&.ext\fR [\fBOPTIONS\fR]
.HP \w'\fBclustalw\fR\ 'u
\fBclustalw\fR [\fB\-help\fR | \fB\-fullhelp\fR]
.SH "DESCRIPTION"
.PP
Clustal\ \&W is a general purpose multiple alignment program for DNA or proteins\&.
.PP
The program 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
\fB\-infile\fR\&.
.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
Output full help 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\-pim\fR
.RS 4
Output percent identity matrix (while calculating the 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
.ps +1
\fBGeneral settings:\fR
.RS 4
.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
.PP
\fB\-maxseqlen=\fR\fB\fIn\fR\fR
.RS 4
Maximum allowed input sequence length\&.
.RE
.PP
\fB\-quiet\fR
.RS 4
Reduce console output to minimum\&.
.RE
.PP
\fB\-stats=\fR\fB\fIfile\fR\fR
.RS 4
Log some alignments statistics to
\fIfile\fR\&.
.RE
.RE
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBFast Pairwise Alignments:\fR
.RS 4
.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
.ps +1
\fBSlow Pairwise Alignments:\fR
.RS 4
.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
.ps +1
\fBMultiple Alignments:\fR
.RS 4
.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
.ps +1
\fBProfile Alignments:\fR
.RS 4
.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
.ps +1
\fBSequence to Profile Alignments:\fR
.RS 4
.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
.ps +1
\fBStructure Alignments:\fR
.RS 4
.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
.ps +1
\fBTrees:\fR
.RS 4
.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\*(Aqs 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
\m[blue]\fB\%http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal\fR\m[]\&.
.SH "SEE ALSO"
.PP
\fBclustalx\fR(1)\&.
.SH "REFERENCES"
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
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)\&.
\m[blue]\fBClustal W and Clustal X version 2\&.0\&.\fR\m[]\&\s-2\u[1]\d\s+2
Bioinformatics, 23, 2947\-2948\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD\&. (2003)\&.
\m[blue]\fBMultiple sequence alignment with the Clustal series of programs\&.\fR\m[]\&\s-2\u[2]\d\s+2
Nucleic Acids Res\&., 31, 3497\-3500\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ\&. (1998)\&.
\m[blue]\fBMultiple sequence alignment with Clustal X\fR\m[]\&\s-2\u[3]\d\s+2\&. Trends Biochem Sci\&., 23, 403\-405\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG\&. (1997)\&.
\m[blue]\fBThe CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools\&.\fR\m[]\&\s-2\u[4]\d\s+2
Nucleic Acids Res\&., 25, 4876\-4882\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Higgins DG, Thompson JD, Gibson TJ\&. (1996)\&.
\m[blue]\fBUsing CLUSTAL for multiple sequence alignments\&.\fR\m[]\&\s-2\u[5]\d\s+2
Methods Enzymol\&., 266, 383\-402\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Thompson JD, Higgins DG, Gibson TJ\&. (1994)\&.
\m[blue]\fBCLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position\-specific gap penalties and weight matrix choice\&.\fR\m[]\&\s-2\u[6]\d\s+2
Nucleic Acids Res\&., 22, 4673\-4680\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Higgins DG\&. (1994)\&.
\m[blue]\fBCLUSTAL V: multiple alignment of DNA and protein sequences\&.\fR\m[]\&\s-2\u[7]\d\s+2
Methods Mol Biol\&., 25, 307\-318
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Higgins DG, Bleasby AJ, Fuchs R\&. (1992)\&.
\m[blue]\fBCLUSTAL V: improved software for multiple sequence alignment\&.\fR\m[]\&\s-2\u[8]\d\s+2
Comput\&. Appl\&. Biosci\&., 8, 189\-191\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Higgins,D\&.G\&. and Sharp,P\&.M\&. (1989)\&.
\m[blue]\fBFast and sensitive multiple sequence alignments on a microcomputer\&.\fR\m[]\&\s-2\u[9]\d\s+2
Comput\&. Appl\&. Biosci\&., 5, 151\-153\&.
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
Higgins,D\&.G\&. and Sharp,P\&.M\&. (1988)\&.
\m[blue]\fBCLUSTAL: a package for performing multiple sequence alignment on a microcomputer\&.\fR\m[]\&\s-2\u[10]\d\s+2
Gene, 73, 237\-244\&.
.RE
.SH "AUTHORS"
.PP
\fBDes Higgins\fR
.RS 4
Copyright holder for Clustal\&.
.RE
.PP
\fBJulie Thompson\fR
.RS 4
Copyright holder for Clustal\&.
.RE
.PP
\fBToby Gibson\fR
.RS 4
Copyright holder for Clustal\&.
.RE
.PP
\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
.RS 4
Prepared this manpage in DocBook XML for the Debian distribution\&.
.RE
.SH "COPYRIGHT"
.br
Copyright \(co 1988\(en2010 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
.br
Copyright \(co 2008\(en2010 Charles Plessy (This manpage)
.br
.PP
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\&.
.PP
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\&.
.PP
You should have received a copy of the GNU Lesser General Public License along with this program\&. If not, see http://www\&.gnu\&.org/licenses/, or on Debian systems,
/usr/share/common\-licenses/LGPL\-3\&.
.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