lastex (1)

Calculate expected numbers of alignments for random sequences.

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  4. lastex: Calculate expected numbers of alignments for random sequences.
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  4. lastex: Calculate expected numbers of alignments for random sequences.

DESCRIPTION

Usage: lastex [options] reference-counts-file query-counts-file [alignments-file] Calculate expected numbers of alignments for random sequences.

Options (default settings): -h: show all options and their default settings -s: strands (2 for DNA, 1 for protein) -r: match score (DNA: 1, protein: blosum62) -q: mismatch cost (DNA: 1, protein: blosum62) -p: match/mismatch score matrix -a: gap existence cost (DNA: 7, protein: 11) -b: gap extension cost (DNA: 1, protein: 2) -g: do calculations for gapless alignments -y: find the expected number of alignments with score >= this -E: maximum expected number of alignments -z: calculate the expected number of alignments per:

  • 0 = reference counts file / query counts file 1 = reference counts file / each query sequence 2 = each reference sequence / query counts file 3 = each reference sequence / each query sequence (0)

REPORTING BUGS

Report bugs to: last-align (ATmark) googlegroups (dot) com

LAST home page: http://last.cbrc.jp/