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
OPTIONS
- -h, --help
-
Display the help message.
- --version
-
Display version information.
Main Options::
- -s, --seq INPUT_FILE
-
Name of multi-fasta input file. Valid filetypes are: .frn, .fna, .ffn, .fasta, .faa, and .fa.
- -a, --alphabet STRING
-
The used sequence alphabet. One of protein, dna, rna, and iupac. Default: protein.
- -o, --outfile OUTPUT_FILE
-
Name of the output file. Valid filetypes are: .msf, .frn, .fna, .ffn, .fasta, .faa, and .fa. Default: out.fasta.
Segment Match Generation Options::
- -m, --method List of STRING's
-
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 List of INPUT_FILE's
-
Name of match file. To select multiple files recall this option with different arguments. Valid filetypes are: .mums, .lib, .blast, and .aln.
- -pa, --pairwise-alignment STRING
-
Pairwise alignment method. Default: unbanded for usual alignments (< 50 sequences), banded for deep alignments (>= 50 sequences) One of unbanded and banded.
- -bw, --band-width INTEGER
-
Band width. This option automatically select banded pairwise alignment (see pa for details) In range [2..inf]. Default: 60.
Scoring Options::
- -g, --gop INTEGER
-
gap open penalty Default: -13.
- -e, --gex INTEGER
-
gap extension penalty Default: -1.
- -ma, --matrix STRING
-
score matrix Default: Blosum62.
- -ms, --msc INTEGER
-
match score Default: 5.
- -mm, --mmsc INTEGER
-
mismatch penalty Default: -4.
Guide Tree Options::
- -u, --usetree STRING
-
Name of the file containing the Newick Guide Tree.
- -b, --build STRING
-
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 INPUT_FILE
-
Name of the alignment file <FASTA FILE> Valid filetypes are: .frn, .fna, .ffn, .fasta, .faa, and .fa.