Hi everyone,
Phangorn package allows to perform ML trees after having chosen a model.
I've run jmodeltest which has told me that a model GTR+G would be
appropriate for my data.
I would like to enter the different parameters in the pml function in
order to draw a tree.
There's an example for pml but I don't fully understand it.
To perform a JC + Gamma + I - model, they do:
fitJC_GI <- update(fitJC, k=4, inv=.2)
I is the the proportion of invariable site, but I don't understand why
.2 is chosen in that exemple.
What would it be if you wanted to perform GTR+G? or +F?
We can fix bf, the base frequencies, and I would like to, but I do not
find how to code it: should I put the different values between brackets?
I hope that my approach is appropriate.
Many thanks in advance for your help.
Erwan Delrieu-Trottin
--
Erwan Delrieu-Trottin, PhD student
USR 3278 CNRS - EPHE
Centre de Biologie et Ecologie Tropicale et Méditerranéenne
Université de Perpignan, 52 Av. Paul Alduy
66860 Perpignan cedex, France
e-mail : erwan.delrieu-trot...@etu.upmc.fr
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