<![CDATA[BOL: Ka, Ks and Ka/Ks calculations]]> https://bioinformaticsonline.com/bookmarks/view/28922/ka-ks-and-kaks-calculations? https://bioinformaticsonline.com/bookmarks/view/28922/ka-ks-and-kaks-calculations Mon, 29 Aug 2016 11:44:11 -0500 https://bioinformaticsonline.com/bookmarks/view/28922/ka-ks-and-kaks-calculations <![CDATA[Ka, Ks and Ka/Ks calculations]]> 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. 

Look for KaKs calculation:

https://github.com/fumba/kaks-calculator

http://longlab.uchicago.edu/?q=gKaKs

http://www.ncbi.nlm.nih.gov/pubmed/23314322

Address of the bookmark: http://longlab.uchicago.edu/?q=gKaKs

]]> Poonam Mahapatra