Provided by: libsmithwaterman0_0.0+git20160702.2610e25-7_amd64
smithwaterman - determine similar regions between two strings or nucleotide or protein sequences
smithwaterman [options] <reference sequence> <query sequence>
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.
-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.
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.