.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH LASTEX "1" "October 2014" "lastex 490" "User Commands"
.SH NAME
lastex \- Calculate expected numbers of alignments for random sequences.
.SH DESCRIPTION
Usage:
lastex [options] reference\-counts\-file query\-counts\-file [alignments\-file]
Calculate expected numbers of alignments for random sequences.
.PP
Options (default settings):
\fB\-h\fR: show all options and their default settings
\fB\-s\fR: strands (2 for DNA, 1 for protein)
\fB\-r\fR: match score   (DNA: 1, protein: blosum62)
\fB\-q\fR: mismatch cost (DNA: 1, protein: blosum62)
\fB\-p\fR: match/mismatch score matrix
\fB\-a\fR: gap existence cost (DNA: 7, protein: 11)
\fB\-b\fR: gap extension cost (DNA: 1, protein:  2)
\fB\-g\fR: do calculations for gapless alignments
\fB\-y\fR: find the expected number of alignments with score >= this
\fB\-E\fR: maximum expected number of alignments
\fB\-z\fR: calculate the expected number of alignments per:
.IP
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)
.SH "REPORTING BUGS"
Report bugs to: last\-align (ATmark) googlegroups (dot) com
.br
LAST home page: http://last.cbrc.jp/