What kind of analysis? To implement models of sequence evolution PAML is very good, but you have to obtain the trees elsewhere.
For Maximum-Likelihood analyses, one of the very best options available is Garli. If you need a fast program (e.g., if your dataset is large), then go with RAxML.
For Bayesian analyses, with no doubt MrBayes. If you would like to infer also time since divergence events using the best possible approach these days (a relaxed-clock approach), then Beast is the way to go.
If you still consider using parsimony for your analyses, then PAUP and TNT are your options. The latter is free and very fast. Opinions vary with regard to which of these two is better (i.e. provides you with the shortest tree), but there is an increasing trend among those who still use parsimony to prefer TNT.
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