seqan_tcoffee - Multiple sequence alignment
seqan_tcoffee -s <FASTA FILE>
[OPTIONS]
SeqAn::T-Coffee is a multiple sequence alignment tool.
(c) Copyright 2009 by Tobias Rausch
- -h, --help
- Display the help message.
- --version
- Display version information.
- -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.
- -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.
- -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.
- -i, --infile
INPUT_FILE
- Name of the alignment file <FASTA FILE> Valid filetypes are:
.frn, .fna, .ffn, .fasta, .faa, and
.fa.