.TH SEQAN_TCOFFEE "1" "September 2009" "Version 1.11 (30. July 2009) Revision: 4637" "User Commands"
.SH NAME
seqan_tcoffee \- Multiple sequence alignment
.SH SYNOPSIS
.B seqan_tcoffee
\fI-s <FASTA sequence file> \fR[\fIOptions\fR]
.SH DESCRIPTION
Multiple sequence alignment \- SeqAn::T\-Coffee
.TP
\fB\-h\fR,  \fB\-\-help\fR
displays this help message
.TP
\fB\-V\fR,  \fB\-\-version\fR
print version information
.SS "Main Options:"
.TP
\fB\-s\fR,  \fB\-\-seq\fR <FASTA Sequence File>
file with sequences
.TP
\fB\-a\fR,  \fB\-\-alphabet\fR [protein | dna | rna]
sequence alphabet (default protein)
.TP
\fB\-o\fR,  \fB\-\-outfile\fR <Filename>
output filename (default out.fasta)
.TP
\fB\-f\fR,  \fB\-\-format\fR [fasta | msf]
output format (default fasta)
.SS "Segment Match Generation Options:"
.TP
\fB\-m\fR,  \fB\-\-method\fR
list of match generation methods
\fR global = Global alignments
\fR local = Local alignments
\fR overlap = Overlap alignments
\fR lcs = Longest common subsequence
\fR Default: global,local
\IP No spaces in\-between.
.TP
\fB\-bl\fR, \fB\-\-blast\fR <File1>,<File2>,...
list of BLAST match files
.TP
\fB\-mu\fR, \fB\-\-mummer\fR <File1>,<File2>,...
list of MUMmer match files
.TP
\fB\-al\fR, \fB\-\-aln\fR <File1>,<File2>,...
list of FASTA align files
.TP
\fB\-li\fR, \fB\-\-lib\fR <File1>,<File2>,...
list of T\-Coffee libraries
.SS "Scoring Options:"
.TP
\fB\-g\fR,  \fB\-\-gop\fR <Int>
gap open penalty (default \fB\-13\fR)
.TP
\fB\-e\fR,  \fB\-\-gex\fR <Int>
gap extension penalty (default \fB\-1\fR)
.TP
\fB\-ma\fR, \fB\-\-matrix\fR <Matrix file>
score matrix (default Blosum62)
.TP
\fB\-ms\fR, \fB\-\-msc\fR <Int>
match score (default 5)
.TP
\fB\-mm\fR, \fB\-\-mmsc\fR <Int>
mismatch penalty (default \fB\-4\fR)
.SS "Guide Tree Options:"
.TP
\fB\-u\fR,  \fB\-\-usetree\fR <Newick guide tree>
tree filename
.TP
\fB\-b\fR,  \fB\-\-build\fR [nj, min, max, avg, wavg]
tree building method (default nj)
\fR nj = Neighbor\-joining
\fR min = UPGMA single linkage
\fR max = UPGMA complete linkage
\fR avg = UPGMA average linkage
\fR wavg = UPGMA weighted average linkage
.IP
Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair.
.SS "Alignment Evaluation Options:"
.TP
\fB\-i\fR,  \fB\-\-infile\fR <FASTA alignment file>
alignment file
.SH AUTHOR
.br
seqan_tcoffee was written by Tobias Rausch.
.PP
This manual page was generated using html2man and polished by
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