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.

is ML "better" than bayes method ?

That is under debate and both are good methods.

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.

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

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.