SYNOPSIS

sdpMatcher query target k [-indelRate delta] [-showalign] [-printsw] [-noRefine] [-indel i] [-local] [-match m] [-sdpIndel i]

DESCRIPTION

Performs sparse dynamic programming (SDP) between pairs of sequences as they are given in two FASTA files, called query and target for convenience. k is the size of the k-mer used for the SDP algorithm.