Provided by: seqan-apps_1.4.1+dfsg-2_amd64 
NAME
seqan_tcoffee - Multiple sequence alignment
SYNOPSIS
seqan_tcoffee -s <FASTA FILE> [OPTIONS]
DESCRIPTION
SeqAn::T-Coffee is a multiple sequence alignment tool.
(c) Copyright 2009 by Tobias Rausch
-h, --help
Displays this help message.
--version
Display version information
Main Options::
-s, --seq FILE
Name of multi-fasta input file. Valid filetypes are: fa, FA, Fa, fasta, FASTA, and Fasta.
-a, --alphabet STR
The used sequence alphabet. One of protein, dna, and rna. Default: protein.
-o, --outfile FILE
Name of the output file. Valid filetypes are: fasta and msf. Default: out.fasta.
Segment Match Generation Options::
-m, --method STR
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.
-l, --libraries FILE
Name of match file. To select multiple files recall this option with different arguments. Valid
filetypes are: blast, mums, aln, and lib.
Scoring Options::
-g, --gop NUM
gap open penalty Default: -13.
-e, --gex NUM
gap extension penalty Default: -1.
-ma, --matrix STR
score matrix Default: Blosum62.
-ms, --msc NUM
match score Default: 5.
-mm, --mmsc NUM
mismatch penalty Default: -4.
Guide Tree Options::
-u, --usetree STR
Name of the file containing the Newick Guide Tree.
-b, --build STR
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.
Alignment Evaluation Options::
-i, --infile FILE
Name of the alignment file <FASTA FILE> Valid filetypes are: fa, FA, Fa, fasta, and FASTA.
VERSION
seqan_tcoffee version: Version 1.11 (30. July 2009) Revision: 4637 Last update July 2012