This is the command seqan_tcoffee that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
-h, --help
Displays this help message.
--version
Display version information
Main Options::
-s, --seq FILE
Name of multi-fasta input file. Valid filetypes are: fa, FA, Fa, fasta, FASTA, and
Fasta.
-a, --alphabet STR
The used sequence alphabet. One of protein, dna, and rna. Default: protein.
-o, --outfile FILE
Name of the output file. Valid filetypes are: fasta and msf. Default: out.fasta.
Segment Match Generation Options::
-m, --method STR
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 FILE
Name of match file. To select multiple files recall this option with different
arguments. Valid filetypes are: blast, mums, aln, and lib.
Scoring Options::
-g, --gop NUM
gap open penalty Default: -13.
-e, --gex NUM
gap extension penalty Default: -1.
-ma, --matrix STR
score matrix Default: Blosum62.
-ms, --msc NUM
match score Default: 5.
-mm, --mmsc NUM
mismatch penalty Default: -4.
Guide Tree Options::
-u, --usetree STR
Name of the file containing the Newick Guide Tree.
-b, --build STR
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 FILE
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
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