NAME

       homology-score.pl - generates homology scorse from murasaki anchor files

SYNOPSIS

       filter.pl [options] <murasaki ailgnment file> [output file]

OPTIONS

        --aligner=<alignment program> => Selects the aligner program.
            Options are clustalw (slow but won't die on large anchors),
            or muscle (fast, but dies on anchors longer than 20k).
            Default is Muscle.