In this talk I will present three new computational methods for phylogenetics: (i) a fast and accurate model selection approach (ModelFinder), (ii) an effective tree reconstruction (IQ-TREE) and (iii) a novel ultrafast bootstrap (UFBoot). These methods represent three key steps in every phylogenetic analysis. I will then apply advanced mixture models to revisit the once hot debate of Coelomata-Ecdysozoa hypotheses in the basal animal phylogeny.