Phylogenetic tree using ML algorithm

Question

[Picasa]

Hi

I am very beginner in this domain and I am looking for some help.

So I have made a multiple alignment with MAFFT. I would like know to infer a philogenetic tree.

I heard about RaXML and I plan to use it.

1) However, which model should I use ? Is there a program that can help me to choose the model ?

2) What are the main differences with Bayes method ?

Thanks a lot.

Answer 1

[Brice Sarver]

You'll want to do model selection on your dataset. Check out MrModelTest or DT-ModSel.

ML phylogenetics produces a point-estimate of the topology (the MLE). Bayesian methods, in addition to being able to specify priors on your analysis, produces a posterior distribution of trees.

[Picasa]

is ML "better" than bayes method ?

[Cacau]

That is under debate and both are good methods.

[Brice Sarver]

If you're calibrating your phylogeny (placing priors on node ages), most Bayesian approaches work better than scaling after the fact. It's not fair to say one is better than the other; they produce different things with different assumptions about how to estimate the phylogeny in the first place.

[Picasa]

From what I understand, bayesian should be use if we know something about our data ( hypothese, model) ?

[Brice Sarver]

Yes, though some models are only implemented in a Bayesian framework (e.g., UCLN vs. strict clock models in BEAST). Also, the default priors are a great starting point in modern approaches and generally perfectly acceptable for publication-worthy analyses. If you can construct informed priors, you should use them - it's a guiding philosophy behind Bayesian analysis.