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: 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/