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.