gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs can automatically detect and eliminate frameshift mutations and premature stop codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset.
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Chengjun Zhang; Jun Wang; Manyuan Long; Chuanzhu Fan
gKaKs: The pipeline for genome level Ka/Ks calculation.
Bioinformatics (2013) 29 (5): 645-646.; doi: 10.1093/bioinformatics/btt009