This code has been stable / in-place since ~2006 and represents work from Jason Stajich's PhD thesis exploring how variation in pairwise suboptimal alignment impact estimations of Ka and Ks for molecular evolution distances.
By far the most useful aspect is rapid pairwise implementation of YN00 estimation of Ka and Ks from alignments into simple tabular output to support quick prototyping and scans of molecular divergence. See yn00_cds_prealigned for that main code as well as yn00_cds_optimal for pairwise alignment calculation from unaligned CDS sequence.