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

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