.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH SEQAN_TCOFFEE "1" "September 2014" "seqan_tcoffee 1.4.1+dfsg" "User Commands"
.SH NAME
seqan_tcoffee \- Multiple sequence alignment
.PP
SYNOPSIS
.IP
seqan_tcoffee \fB\-s\fR <FASTA FILE> [OPTIONS]
.PP
DESCRIPTION
.IP
SeqAn::T\-Coffee is a multiple sequence alignment tool.
.IP
(c) Copyright 2009 by Tobias Rausch
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
Main Options::
.HP
\fB\-s\fR, \fB\-\-seq\fR FILE
.IP
Name of multi\-fasta input file. Valid filetypes are: fa, FA, Fa,
fasta, FASTA, and Fasta.
.HP
\fB\-a\fR, \fB\-\-alphabet\fR STR
.IP
The used sequence alphabet. One of protein, dna, and rna. Default:
protein.
.HP
\fB\-o\fR, \fB\-\-outfile\fR FILE
.IP
Name of the output file. Valid filetypes are: fasta and msf.
Default: out.fasta.
.IP
Segment Match Generation Options::
.HP
\fB\-m\fR, \fB\-\-method\fR STR
.IP
Defines the generation method for matches. To select multiple
generation methods recall this option with different arguments. One
of global, local, overlap, and lcs. Default: global and local.
.HP
\fB\-l\fR, \fB\-\-libraries\fR FILE
.IP
Name of match file. To select multiple files recall this option with
different arguments. Valid filetypes are: blast, mums, aln, and lib.
.IP
Scoring Options::
.HP
\fB\-g\fR, \fB\-\-gop\fR NUM
.IP
gap open penalty Default: \fB\-13\fR.
.HP
\fB\-e\fR, \fB\-\-gex\fR NUM
.IP
gap extension penalty Default: \fB\-1\fR.
.HP
\fB\-ma\fR, \fB\-\-matrix\fR STR
.IP
score matrix Default: Blosum62.
.HP
\fB\-ms\fR, \fB\-\-msc\fR NUM
.IP
match score Default: 5.
.HP
\fB\-mm\fR, \fB\-\-mmsc\fR NUM
.IP
mismatch penalty Default: \fB\-4\fR.
.IP
Guide Tree Options::
.HP
\fB\-u\fR, \fB\-\-usetree\fR STR
.IP
Name of the file containing the Newick Guide Tree.
.HP
\fB\-b\fR, \fB\-\-build\fR STR
.IP
Method to build the tree. Following methods are provided:
Neighbor\-Joining (nj), UPGMA single linkage (min), UPGMA complete
linkage (max), UPGMA average linkage (avg), UPGMA weighted average
linkage (wavg). Neighbor\-Joining creates an unrooted tree, which we
root at the last joined pair. One of nj, min, max, avg, and wavg.
Default: nj.
.IP
Alignment Evaluation Options::
.HP
\fB\-i\fR, \fB\-\-infile\fR FILE
.IP
Name of the alignment file <FASTA FILE> Valid filetypes are: fa, FA,
Fa, fasta, and FASTA.
.PP
VERSION
.IP
seqan_tcoffee version: Version 1.11 (30. July 2009) Revision: 4637
Last update July 2012