Question: does the best substitution model for a phylogeny tree differ between one method to the other ?
0
gravatar for Michel Edwar
5.2 years ago by
Michel Edwar70
Sweden
Michel Edwar70 wrote:

I am using MrBayes, PhyML and phangorn to build the trees for a certain data set. I have used ProtTest  and it identified LG+I+G+F to be the best substitution model for the maximum likelihood method ( PhML).  My question is,  can i use the same substitution model in Mr Bayes (Bayesin analysis ) and phangorn (nearest neighbor) , or do I need a different test for each method ? 

 

 

 

 

 

 

 

 

 

ADD COMMENTlink modified 5.2 years ago by h.mon30k • written 5.2 years ago by Michel Edwar70
0
gravatar for h.mon
5.2 years ago by
h.mon30k
Brazil
h.mon30k wrote:

You may use the same model for MrBayes (if possible to specify this model in MrBayes), or use MrAIC to find the best model.

Nearest-neighbour is a method to perform tree rearrangement to search the parameter space, no relation to the evolutionary model you choose.

ADD COMMENTlink written 5.2 years ago by h.mon30k

but in MAFFT server, you can identify one of three substitution models for neighbor joining method.

[Substitution model (valid when NJ is selected): JTT
WAG Alpha
Poisson]

ADD REPLYlink modified 9 months ago by RamRS28k • written 5.2 years ago by Michel Edwar70

Not all programs implement all models. For example, I do not know if the latest MrBayes implement all models tested with ModelTest, I know an earlier version (I think 3.1 but may be wrong) implemented only a subset of the models found in ModelTest.

Anyway, if you are doing ML and bayesian phylogenetic inference, there is no need for NJ, which in general is less accurate.

ADD REPLYlink written 5.2 years ago by h.mon30k
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