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