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) Revision: 463September 2009                         SEQAN_TCOFFEE(1)