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).