Bias and likelihood

James O. McInerney james.o.mcinerney at may.ie
Wed Jun 2 14:59:48 EST 1999


Jean-Francois Martin wrote:
> 
> In butterfly mtDNA, the composition bias is extreme toward A-T (80 to 90%
> depending on gene and codon position).
> It seems also unlikely that every kind of substitution has equal probability
> to occur.
> 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?
> 

Jean-Francois,

There has been a wonderful advance recently in work towards
non-homogenous ML models, led by your own compatriots in Lyon.

Nicolas Galtier and Manolo Gouy have developed a model and accompanying
program for using a non-homogenous ML model in order to infer
phylogenies. It is possible, using this method to allow for variation in
base composition across lineages in the tree.

It has been a little while since I read the paper, so I'm a bit rusty on
the specifics and I don't have the paper to hand, however, you can see
the reference at:

http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9656487&form=6&db=m&Dopt=b


They then went on to use the method in:

http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9880254&form=6&db=m&Dopt=b


You can pick up the program at:

ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/nhml/


Hope this helps,

James
-- 
             Dr. James O. McInerney,
Dept. Biology,                       Dept. Zoology,
Natl. Univ. Ireland,                 The Natural History Museum,
Maynooth,                  and       Cromwell road,
Co. Kildare, Ireland                 London SW7 5BD, UK.
Phone +353 1 708 3860                +44 171 938 9163
Fax   +353 1 708 3845                +44 171 938 9158
email james.o.mcinerney at may.ie       j.mcinerney at nhm.ac.uk




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