xenial (1) seqan_tcoffee.1.gz

Provided by: seqan-apps_1.4.1+dfsg-2_amd64 bug

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