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/