SYNOPSIS

smithwaterman [options] <reference sequence> <query sequence>

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.

OPTIONS

-m, --match-score

the match score (default 10.0)

-n, --mismatch-score

the mismatch score (default -9.0)

-g, --gap-open-penalty

the gap open penalty (default 15.0)

-z, --entropy-gap-open-penalty

enable entropy scaling of the gap open penalty

-e, --gap-extend-penalty

the gap extend penalty (default 6.66)

-r, --repeat-gap-extend-penalty

use repeat information when generating gap extension penalties

-b, --bandwidth

bandwidth to use (default 0, or non-banded algorithm)

-p, --print-alignment

print out the alignment

-R, --reverse-complement

report the reverse-complement alignment if it scores better

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.

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.