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Question: Phylogenetic tree using ML algorithm
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gravatar for Picasa
4.2 years ago by
Picasa • 590
Picasa • 590 wrote:

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.
ml phylogenie • 992 views
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modified 4.2 years ago by Brice Sarver • 3.6k • written 4.2 years ago by Picasa • 590
1
gravatar for Brice Sarver
4.2 years ago by
Brice Sarver • 3.6k
United States
Brice Sarver • 3.6k wrote:

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.
ADD COMMENT • link written 4.2 years ago by Brice Sarver • 3.6k

is ML "better" than bayes method ?

ADD REPLY • link written 4.2 years ago by Picasa • 590

That is under debate and both are good methods.

ADD REPLY • link written 4.2 years ago by Cacau • 480

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.

ADD REPLY • link written 4.2 years ago by Brice Sarver • 3.6k

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

ADD REPLY • link modified 4.2 years ago • written 4.2 years ago by Picasa • 590

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.

ADD REPLY • link written 4.2 years ago by Brice Sarver • 3.6k
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