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

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options::
       -s, --seq INPUT_FILE
              Name  of  multi-fasta  input  file.  Valid filetypes are: .frn, .fna, .ffn, .fasta,
              .faa, and .fa.

       -a, --alphabet STRING
              The used sequence alphabet. One of protein, dna, rna, and iupac. Default: protein.

       -o, --outfile OUTPUT_FILE
              Name of the output file. Valid filetypes are: .msf, .frn, .fna, .ffn, .fasta, .faa,
              and .fa. Default: out.fasta.

   Segment Match Generation Options::
       -m, --method List of STRING's
              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 List of INPUT_FILE's
              Name  of  match  file.  To  select multiple files recall this option with different
              arguments. Valid filetypes are: .mums, .lib, .blast, and .aln.

       -pa, --pairwise-alignment STRING
              Pairwise alignment method. Default: unbanded for usual alignments (< 50 sequences),
              banded for deep alignments (>= 50 sequences) One of unbanded and banded.

       -bw, --band-width INTEGER
              Band  width. This option automatically select banded pairwise alignment (see pa for
              details) In range [2..inf]. Default: 60.

   Scoring Options::
       -g, --gop INTEGER
              gap open penalty Default: -13.

       -e, --gex INTEGER
              gap extension penalty Default: -1.

       -ma, --matrix STRING
              score matrix Default: Blosum62.

       -ms, --msc INTEGER
              match score Default: 5.

       -mm, --mmsc INTEGER
              mismatch penalty Default: -4.

   Guide Tree Options::
       -u, --usetree STRING
              Name of the file containing the Newick Guide Tree.

       -b, --build STRING
              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 INPUT_FILE
              Name of the alignment file <FASTA FILE> Valid  filetypes  are:  .frn,  .fna,  .ffn,
              .fasta, .faa, and .fa.