debian man page for lastex

LASTEX(1)							   User Commands							 LASTEX(1)

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, pro-
       tein: 11) -b: gap extension cost (DNA: 1, protein:  2) -g: do calculations for gapless alignments -y: find the expected	number	of  align-
       ments 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 (ATmark) cbrc (dot) jp
       LAST home page: http://last.cbrc.jp/

lastex 199							     May 2012								 LASTEX(1)