NAME
seqan_tcoffee - Multiple sequence alignment
SYNOPSIS
seqan_tcoffee -s <FASTA sequence file> [Options]
DESCRIPTION
Multiple sequence alignment - SeqAn::T-Coffee
-h, --help
displays this help message
-V, --version
print version information
Main Options:
-s, --seq <FASTA Sequence File>
file with sequences
-a, --alphabet [protein | dna | rna]
sequence alphabet (default protein)
-o, --outfile <Filename>
output filename (default out.fasta)
-f, --format [fasta | msf]
output format (default fasta)
Segment Match Generation Options:
-m, --method
list of match generation methods
global = Global alignments
local = Local alignments
overlap = Overlap alignments
lcs = Longest common subsequence
Default: global,local IP No spaces in-between.
-bl, --blast <File1>,<File2>,...
list of BLAST match files
-mu, --mummer <File1>,<File2>,...
list of MUMmer match files
-al, --aln <File1>,<File2>,...
list of FASTA align files
-li, --lib <File1>,<File2>,...
list of T-Coffee libraries
Scoring Options:
-g, --gop <Int>
gap open penalty (default -13)
-e, --gex <Int>
gap extension penalty (default -1)
-ma, --matrix <Matrix file>
score matrix (default Blosum62)
-ms, --msc <Int>
match score (default 5)
-mm, --mmsc <Int>
mismatch penalty (default -4)
Guide Tree Options:
-u, --usetree <Newick guide tree>
tree filename
-b, --build [nj, min, max, avg, wavg]
tree building method (default nj)
nj = Neighbor-joining
min = UPGMA single linkage
max = UPGMA complete linkage
avg = UPGMA average linkage
wavg = UPGMA weighted average linkage
Neighbor-joining creates an unrooted tree. We root that tree at
the last joined pair.
Alignment Evaluation Options:
-i, --infile <FASTA alignment file>
alignment file
AUTHOR
seqan_tcoffee was written by Tobias Rausch.
This manual page was generated using html2man and polished by Soeren
Sonnenburg <sonne@debian.org>, for the Debian project (but may be used
by others).
Version 1.11 (30. July 2009) RevSeptember32009