sdpMatcher1
Nucleotide sequence matching using sparse dynamic programming
Usage
sdpMatcher query
target
k
[-indelRate
delta]
[-showalign]
[-printsw]
[-noRefine]
[-indel
i]
[-local]
[-match
m]
[-sdpIndel
i]
Overview
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.