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.