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.
Categorising sites alone is not quite what I have in mind. I want to
categorise a site and evaluate the probability of observing this site
for model X (say) given a particular topology and branch lengths. And
for sites from the other category I want to slightly change the model
and evaluate the probability of observing this site for model Y (say).
The likelihood of the tree then becomes the product of all of these
likelihoods (even though the likelihoods were derived from different
The motivation for doing all of this is purely biological...one model
does not adequately describe what I think is happening during the
evolution of all of the gene.
Is this possible?
Dr. James O. McInerney Ph.D. Phone/Voicemail: +44 171 938 9247
Senior Scientific Officer, email:j.mcinerney at nhm.ac.uk
The Natural History Museum,
London SW7 5BD
Whenever I think of the past, it brings back so many memories...