NAME

       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:
       file for residue pair scores -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/

lastex 393                                        January 2014                                         LASTEX(1)