.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH SMITHWATERMAN "1" "June 2016" "smithwaterman 0.0+20151117" "User Commands"
.SH NAME
smithwaterman \- determine similar regions between two strings or nucleotide or protein sequences
.SH SYNOPSIS
.B smithwaterman
[options] <reference sequence> <query sequence>
.SH DESCRIPTION
The Smith–Waterman algorithm performs local sequence alignment; that is,
for determining similar regions between two strings or nucleotide or
protein sequences. Instead of looking at the total sequence, the
Smith–Waterman algorithm compares segments of all possible lengths and
optimizes the similarity measure.
.SH OPTIONS
.TP
\fB\-m\fR, \fB\-\-match\-score\fR
the match score (default 10.0)
.TP
\fB\-n\fR, \fB\-\-mismatch\-score\fR
the mismatch score (default \fB\-9\fR.0)
.TP
\fB\-g\fR, \fB\-\-gap\-open\-penalty\fR
the gap open penalty (default 15.0)
.TP
\fB\-z\fR, \fB\-\-entropy\-gap\-open\-penalty\fR
enable entropy scaling of the gap open penalty
.TP
\fB\-e\fR, \fB\-\-gap\-extend\-penalty\fR
the gap extend penalty (default 6.66)
.TP
\fB\-r\fR, \fB\-\-repeat\-gap\-extend\-penalty\fR
use repeat information when generating gap extension penalties
.TP
\fB\-b\fR, \fB\-\-bandwidth\fR
bandwidth to use (default 0, or non\-banded algorithm)
.TP
\fB\-p\fR, \fB\-\-print\-alignment\fR
print out the alignment
.TP
\fB\-R\fR, \fB\-\-reverse\-complement\fR
report the reverse\-complement alignment if it scores better
.PP
When called with literal reference and query sequences, smithwaterman
prints the cigar match positional string and the match position for the
query sequence against the reference sequence.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.