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

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Main Options::

Name of multi-fasta input file. Valid filetypes are: fa, FA, Fa, fasta, FASTA, and Fasta.

The used sequence alphabet. One of protein, dna, and rna. Default: protein.

Name of the output file. Valid filetypes are: fasta and msf. Default: out.fasta.

Segment Match Generation Options::

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.

Name of match file. To select multiple files recall this option with different arguments. Valid filetypes are: blast, mums, aln, and lib.

Scoring Options::

gap open penalty Default: -13.

gap extension penalty Default: -1.

score matrix Default: Blosum62.

match score Default: 5.

mismatch penalty Default: -4.

Guide Tree Options::

Name of the file containing the Newick Guide Tree.

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::

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