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.
>james
>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
ftp.bio.indiana.edu/molbio/evolve.
Ziheng Yang
