SEQAN_TCOFFEE(1)

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 SEQAN_TCOFFEE(1)