---
name: "lastex"
section: "1"
platform: "linux"
package: "last-align"
version: "490-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/lastex"
---

# lastex(1)

Calculate expected numbers of alignments for random sequences.

## 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/