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Bias and likelihood

Marc Robinson marc.robinson at ens-lyon.fr
Wed Jun 2 14:59:09 EST 1999

"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 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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