NAME

       jaligner - Smith-Waterman algorithm with Gotoh's improvement

SYNOPSIS

       jaligner <s1> <s2> <matrix> <open> <extend>

       Or just type jaligner to see the GUI.

EXAMPLES

       jaligner p53_{human,mouse}.fasta BLOSUM62 10 0.5

HOMEPAGE

       http://jaligner.sourceforge.net/

                                                                                                     JALIGNER(1)