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TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). Methods available include model selection and phylogenetic tree estimation using the Bayesian inference and maximum likelihood (ML) approaches, in addition to recombination detectiondoi:10.1093/bioinformatics/btn575 pmid:18984599 pmcid:PMC2638937 fatcat:ymvgx4hs5zfbtefdpq45fxwloi