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.