NAME

       smithwaterman - determine similar regions between two strings or nucleotide or protein sequences

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.