title: gKaKs: the pipeline for genome-level Ka/Ks calculation.
abstract: CONCLUSIONS
  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. It is especially useful for newly sequenced genomes that have not been well annotated. We applied gKaKs to estimate the genome-wide substitution rates in five pairs of closely related species. The average Ka and Ks computed by gKaKs were consistent with previous studies. We also compared the Ka, Ks and Ka/Ks of mouse and rat orthologous protein-coding genes estimated by gKaKs and based on the alignments generated by PAL2NAL. Results from two methods are compatible.
  
  
  METHODS
  gKaKs is implemented in Perl and is freely available on http://longlab.uchicago.edu/?q=gKaKs. The detailed user manual is available on the website.
authors: Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
authors: Chengjun
authors: C
authors: Zhang
authors: Jun
authors: J
authors: Wang
authors: Manyuan
authors: M
authors: Long
authors: Chuanzhu
authors: C
authors: Fan
mesh_terms: D000818:Animals; D003062:Codon; D018388:Codon, Terminator; D016368:Frameshift Mutation; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D051381:Rats; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D003062:Codon; D018388:Codon, Terminator