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other versions
- stretch 2.3.1+dfsg-4
- testing 2.4.0+dfsg-11
- stretch-backports 2.4.0+dfsg-11~bpo9+1
- unstable 2.4.0+dfsg-11
SEQAN_TCOFFEE(1) | User Commands | SEQAN_TCOFFEE(1) |
NAMEΒΆ
seqan_tcoffee - Multiple sequence alignmentSYNOPSIS
- 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-check BOOL
- Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.
--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, and rna. 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.
VERSION
- Last update: seqan_tcoffee version: 1.13.6 [tarball] SeqAn version: 2.3.1
June 2017 | seqan_tcoffee 2.3.1+dfsg-4 |