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.\" Title: KALIGN
.\" Author: Timo Lassmann <timolassmann@gmail.com>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
.\" Date: February 17, 2007
.\" Manual: Kalign User Manual
.\" Source: kalign 2.03
.\"
.TH "KALIGN" "1" "February 17, 2007" "kalign 2.03" "Kalign User Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
kalign - performs multiple alignment of biological sequences.
.SH "SYNOPSIS"
.HP 7
\fBkalign\fR [\fIinfile\.fasta\fR] [\fIoutfile\.fasta\fR] [Options]
.HP 7
\fBkalign\fR [\-i\ \fIinfile\.fasta\fR] [\-o\ \fIoutfile\.fasta\fR] [Options]
.HP 7
\fBkalign\fR [<\ \fIinfile\.fasta\fR] [>\ \fIoutfile\.fasta\fR] [Options]
.SH "DESCRIPTION"
.PP
\fBKalign\fR
is a command line tool to perform multiple alignment of biological sequences\. It employs the Wu\-Manber string\-matching algorithm, to improve both the accuracy and speed of the alignment\. It uses global, progressive alignment approach, enriched by employing an approximate string\-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment\. In comparisons made by its authors, Kalign was about 10 times faster than ClustalW and, depending on the alignment size, up to 50 times faster than popular iterative methods\.
.SH "OPTIONS"
.PP
\fB\-s\fR \fB\-gpo\fR \fB\-gapopen\fR \fB\-gap_open\fR \fIx\fR
.RS 4
Gap open penalty
\.
.RE
.PP
\fB\-e\fR \fB\-gpe\fR \fB\-gap_ext\fR \fB\-gapextension\fR \fIx\fR
.RS 4
Gap extension penalty\.
.RE
.PP
\fB\-t\fR \fB\-tgpe\fR \fB\-terminal_gap_extension_penalty\fR \fIx\fR
.RS 4
Terminal gap penalties\.
.RE
.PP
\fB\-m\fR \fB\-bonus\fR \fB\-matrix_bonus\fR \fIx\fR
.RS 4
A constant added to the substitution matrix\.
.RE
.PP
\fB\-c\fR \fB\-sort\fR \fI<input, tree, gaps\.>\fR
.RS 4
The order in which the sequences appear in the output alignment\.
.RE
.PP
\fB\-g\fR \fB\-feature\fR
.RS 4
Selects feature mode and specifies which features are to be used: e\.g\. all, maxplp, STRUCT, PFAM\-A\.\.\.\.
.RE
.PP
\fB\-d\fR \fB\-distance\fR \fI<wu, pair>\fR
.RS 4
Distance method
.RE
.PP
\fB\-b\fR \fB\-tree\fR \fB\-guide\-tree\fR \fI<nj, upgma>\fR
.RS 4
Guide tree method\.
.RE
.PP
\fB\-z\fR \fB\-zcutoff\fR
.RS 4
Parameter used in the wu\-manber based distance calculation\.
.RE
.PP
\fB\-i\fR \fB\-in\fR \fB\-input\fR
.RS 4
Name of the input file\.
.RE
.PP
\fB\-o\fR \fB\-out\fR \fB\-output\fR
.RS 4
Name of the output file\.
.RE
.PP
\fB\-f\fR \fB\-format\fR \fI<fasta, msf, aln, clu, macsim>\fR
.RS 4
The output format\.
.RE
.PP
\fB\-q\fR \fB\-quiet\fR
.RS 4
Print nothing to STDERR\. Read nothing from STDIN\.
.RE
.SH "REFERENCE"
.PP
Please cite Timo Lassmann and Erik L\.L\. Sonnhammer (2005) Kalign \- an accurate and fast multiple sequence alignment algorithm\. BMC Bioinformatics 6:298
.SH "AUTHORS"
.PP
\fBTimo Lassmann\fR <\&timolassmann@gmail\.com\&>
.sp -1n
.IP "" 4
Upstream author of kalign\.
.PP
\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&>
.sp -1n
.IP "" 4
Wrote the manpage\.
.SH "COPYRIGHT"
Copyright \(co 2004, 2005, 2006 Timo Lassmann
.br
.PP
Kalign is free software\. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation\.
.PP
This manual page was written by Charles Plessy
<charles\-debian\-nospam@plessy\.org>
for the
Debian(TM)
system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the same terms as kalign itself\.
.PP
On Debian systems, the complete text of the GNU General Public License can be found in
\fI/usr/share/common\-licenses/GPL\fR\.
.sp
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