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).