ML question

Ziheng Yang ziheng at mws4.biol.berkeley.edu
Thu Sep 19 17:56:20 EST 1996

On 19 Sept, Dr. James O. McInerney Ph.D. wrote:

>Is there a way of calculating a likelihood topology for a gene where
>there is more than one model of sequence evolution.  For instance some
>parts of the gene are evolving with a higher transition/transversion
>ratio than others (say, stems in a tRNA as opposed to loops).  So you
>want to incorporate all of this information into your model.
This sounds similar to something I did before (Yang 1996. Maximum likelihood models 
for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596).  In my 
case, I wanted to analyze sites from the three codon positions as one data set, but 
the three codon positions have different evolutionary rates, transition/transversion 
rate ratios, and base frequencies.  So I made up a few models that account for these 
features.  If you can tell which category each site belongs to (as one can tell 
which codon position each site is from), you might try some of these models.  The 
program is baseml in my PAML package, not so very user-friendly, available at 
Ziheng Yang

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