.TH SEQAN_TCOFFEE 1 "" "seqan_tcoffee 1.13.8 [tarball]" ""
.SH NAME
seqan_tcoffee \- Multiple sequence alignment
.SH SYNOPSIS
\fBseqan_tcoffee\fP -s <\fIFASTA FILE\fP> [\fIOPTIONS\fP]
.SH DESCRIPTION
SeqAn::T-Coffee is a multiple sequence alignment tool.
.sp
(c) Copyright 2009 by Tobias Rausch
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Main Options::
.TP
\fB-s\fP, \fB--seq\fP \fIINPUT_FILE\fP
Name of multi-fasta input file. Valid filetypes are: \fI.frn\fP, \fI.fna\fP, \fI.ffn\fP, \fI.fasta\fP, \fI.faa\fP, and \fI.fa\fP.
.TP
\fB-a\fP, \fB--alphabet\fP \fISTRING\fP
The used sequence alphabet. One of \fIprotein\fP, \fIdna\fP, \fIrna\fP, and \fIiupac\fP. Default: \fIprotein\fP.
.TP
\fB-o\fP, \fB--outfile\fP \fIOUTPUT_FILE\fP
Name of the output file. Valid filetypes are: \fI.msf\fP, \fI.frn\fP, \fI.fna\fP, \fI.ffn\fP, \fI.fasta\fP, \fI.faa\fP, and \fI.fa\fP. Default: \fIout.fasta\fP.
.SS Segment Match Generation Options::
.TP
\fB-m\fP, \fB--method\fP List of \fISTRING\fP's
Defines the generation method for matches. To select multiple generation methods recall this option with different arguments.  One of \fIglobal\fP, \fIlocal\fP, \fIoverlap\fP, and \fIlcs\fP. Default: \fIglobal\fP and \fIlocal\fP.
.TP
\fB-l\fP, \fB--libraries\fP List of \fIINPUT_FILE\fP's
Name of match file. To select multiple files recall this option with different arguments. Valid filetypes are: \fI.mums\fP, \fI.lib\fP, \fI.blast\fP, and \fI.aln\fP.
.TP
\fB-pa\fP, \fB--pairwise-alignment\fP \fISTRING\fP
Pairwise alignment method. Default: \fIunbanded\fP for usual alignments (< 50 sequences), \fIbanded\fP for deep alignments (>= 50 sequences) One of \fIunbanded\fP and \fIbanded\fP.
.TP
\fB-bw\fP, \fB--band-width\fP \fIINTEGER\fP
Band width. This option automatically select \fIbanded\fP pairwise alignment (see \fBpa\fP for details) In range [2..inf]. Default: \fI60\fP.
.SS Scoring Options::
.TP
\fB-g\fP, \fB--gop\fP \fIINTEGER\fP
gap open penalty Default: \fI-13\fP.
.TP
\fB-e\fP, \fB--gex\fP \fIINTEGER\fP
gap extension penalty Default: \fI-1\fP.
.TP
\fB-ma\fP, \fB--matrix\fP \fISTRING\fP
score matrix Default: \fIBlosum62\fP.
.TP
\fB-ms\fP, \fB--msc\fP \fIINTEGER\fP
match score Default: \fI5\fP.
.TP
\fB-mm\fP, \fB--mmsc\fP \fIINTEGER\fP
mismatch penalty Default: \fI-4\fP.
.SS Guide Tree Options::
.TP
\fB-u\fP, \fB--usetree\fP \fISTRING\fP
Name of the file containing the \fINewick Guide Tree\fP.
.TP
\fB-b\fP, \fB--build\fP \fISTRING\fP
Method to build the tree. Following methods are provided: \fINeighbor-Joining\fP (\fBnj\fP), \fIUPGMA single linkage\fP (\fBmin\fP), \fIUPGMA complete linkage\fP (\fBmax\fP), \fIUPGMA average linkage\fP (\fBavg\fP), \fIUPGMA weighted average linkage\fP (\fBwavg\fP). \fINeighbor-Joining\fP creates an unrooted tree, which we root at the last joined pair. One of \fInj\fP, \fImin\fP, \fImax\fP, \fIavg\fP, and \fIwavg\fP. Default: \fInj\fP.
.SS Alignment Evaluation Options::
.TP
\fB-i\fP, \fB--infile\fP \fIINPUT_FILE\fP
Name of the alignment file <\fIFASTA FILE\fP> Valid filetypes are: \fI.frn\fP, \fI.fna\fP, \fI.ffn\fP, \fI.fasta\fP, \fI.faa\fP, and \fI.fa\fP.