"Jean-François Martin" wrote:
>> Furthermore a selection against substitutions providing G and C, which has
> been demonstrated in Dloop of mammalians (A-T rich), is not correctly
> represented by ML models. At least for what I know about Maximum Likelihood
> and PAUP* options, it is impossible to use a non reversible model. Even if
> it was possible, what kind of weighting sheme could fit to the actual (not
> the observed) substitution pattern?
you might want to look at :
Galtier N, et al.
Inferring pattern and process: maximum-likelihood
implementation of a nonhomogeneous model of DNA sequence
evolution for phylogenetic analysis.
Mol Biol Evol. 1998 Jul;15(7):871-9.
hope this helps
Marc
_______________________________________________________
Marc Robinson
Laboratoire de Biologie Moleculaire et Cellulaire
Ecole Normale Superieure de Lyon
46, allee d'Italie tel : +33-4 72 72 86 45
69364 LYON cedex 07 fax : +33-4 72 72 80 80
France e-mail : marc.robinson at ens-lyon.fr
"La liberte ne s'use que quand on ne s'en sert pas."
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