There are a growing number of biological questions that can be answered by analysing multiple sequence alignment data. We have extended the original TOPALi Java application, beyond recombination detection, to launch a range of statistical and evolutionary analyses of multiple sequence alignments as web services. The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.
