.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH GAPCLEANER "1" "December 2015" "gapcleaner 1.15.9" "User Commands"
.SH NAME
gapcleaner \- Find the most-parsimonious ordering of indels
.SH SYNOPSIS
.B gapcleaner
\fI\,<multi-FASTA or Stockholm alignment>\/\fR
.SH DESCRIPTION
gapcleaner from FSA 1.15.9
.PP
Find the most\-parsimonious ordering of indels.
Finds the minimal chain decomposition of the POSET of the alignment;
this corresponds to minimizing the number of gap\-openings across the sequences.
.PP
Input protein alignment must be in multi\-FASTA or Stockholm format.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.