Question: Phylogenetic tree using ML algorithm
0
gravatar for Picasa
4.2 years ago by
Picasa590
Picasa590 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
ADD COMMENTlink modified 4.2 years ago by Brice Sarver3.6k • written 4.2 years ago by Picasa590
1
gravatar for Brice Sarver
4.2 years ago by
Brice Sarver3.6k
United States
Brice Sarver3.6k 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 COMMENTlink written 4.2 years ago by Brice Sarver3.6k

is ML "better" than bayes method ?

ADD REPLYlink written 4.2 years ago by Picasa590

That is under debate and both are good methods.

ADD REPLYlink written 4.2 years ago by Cacau480

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 REPLYlink written 4.2 years ago by Brice Sarver3.6k

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

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Picasa590

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 REPLYlink written 4.2 years ago by Brice Sarver3.6k
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