NAME

       seqan_tcoffee - Multiple sequence alignment

       SYNOPSIS

              seqan_tcoffee -s <FASTA FILE> [OPTIONS]

       DESCRIPTION

              SeqAn::T-Coffee is a multiple sequence alignment tool.

              (c) Copyright 2009 by Tobias Rausch

       -h, --help

              Displays this help message.

       --version

              Display version information

              Main Options::

       -s, --seq FILE

              Name  of multi-fasta input file. Valid filetypes are: fa, FA, Fa, fasta, FASTA, and
              Fasta.

       -a, --alphabet STR

              The used sequence alphabet. One of protein, dna, and rna. Default: protein.

       -o, --outfile FILE

              Name of the output file. Valid filetypes are: fasta and msf.  Default: out.fasta.

              Segment Match Generation Options::

       -m, --method STR

              Defines the generation method for matches. To select  multiple  generation  methods
              recall  this  option  with  different arguments. One of global, local, overlap, and
              lcs. Default: global and local.

       -l, --libraries FILE

              Name of match file. To select multiple files  recall  this  option  with  different
              arguments. Valid filetypes are: blast, mums, aln, and lib.

              Scoring Options::

       -g, --gop NUM

              gap open penalty Default: -13.

       -e, --gex NUM

              gap extension penalty Default: -1.

       -ma, --matrix STR

              score matrix Default: Blosum62.

       -ms, --msc NUM

              match score Default: 5.

       -mm, --mmsc NUM

              mismatch penalty Default: -4.

              Guide Tree Options::

       -u, --usetree STR

              Name of the file containing the Newick Guide Tree.

       -b, --build STR

              Method  to  build  the tree. Following methods are provided: Neighbor-Joining (nj),
              UPGMA single linkage (min), UPGMA complete linkage  (max),  UPGMA  average  linkage
              (avg),  UPGMA weighted average linkage (wavg). Neighbor-Joining creates an unrooted
              tree, which we root at the last joined pair. One of nj, min, max,  avg,  and  wavg.
              Default: nj.

              Alignment Evaluation Options::

       -i, --infile FILE

              Name of the alignment file <FASTA FILE> Valid filetypes are: fa, FA, Fa, fasta, and
              FASTA.

       VERSION

              seqan_tcoffee version: Version 1.11 (30. July 2009) Revision: 4637 Last update July
              2012