.\"     Title: KALIGN
.\"    Author: Timo Lassmann <timolassmann@gmail.com>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
.\"      Date: February 25, 2009
.\"    Manual: Kalign User Manual
.\"    Source: kalign 2.04
.\"
.TH "KALIGN" "1" "February 25, 2009" "kalign 2.04" "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 Muth?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\&.
.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\-same_feature_score\fR
.RS 4
Score for aligning same features\&.
.RE
.PP
\fB\-diff_feature_score\fR
.RS 4
Penalty for aligning different features\&.
.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\-a\fR \fB\-gap_inc\fR
.RS 4
Increases gap penalties depending on the number of existing gaps\&.
.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 "REFERENCES"
.sp
.RS 4
\h'-04'\(bu\h'+03'Timo Lassmann and Erik L\&.L\&. Sonnhammer (2005) Kalign \- an accurate and fast multiple sequence alignment algorithm\&. BMC Bioinformatics 6:298
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'Timo Lassmann, Oliver Frings and Erik L\&. L\&. Sonnhammer (2009) Kalign2: high\-performance multiple alignment of protein and nucleotide sequences allowing external features\&. Nucleic Acid Research 3:858?865\&.
.RE
.SH "AUTHORS"
.PP
\fBTimo Lassmann\fR <\&timolassmann@gmail\&.com\&>
.sp -1n
.IP "" 4
Upstream author of Kalign\&.
.PP
\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
.sp -1n
.IP "" 4
Wrote the manpage\&.
.SH "COPYRIGHT"
Copyright \(co 2004, 2005, 2006, 2007, 2008 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
<plessy@debian\&.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 version 2 can be found in
\fI/usr/share/common\-licenses/GPL\-2\fR\&.
.sp