how to perform a Ka/Ks test

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ryan_m
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how to perform a Ka/Ks test

Many people discuss use of the Ka/Ks value (and likelihood ratio test) to address the protein coding potential of genomic sequence as well as identifying sequences that have undergone positive Darwinian selection. The following paper has one of the better descriptions of how one would accomplish this. One addition I would suggest is the use of "RevTrans" ( Nucleic Acids Res. 2003 Jul 1;31(13):3537-9.) to align the open reading frames.

Ka/Ks paper

ryan_m
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This site may also be useful

This site may also be useful (I haven't tried it yet). It appears to promise a web server to perform Ka/Ks measurement and prediction of positive/purifying selection.

Selection Server