TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

TLDR

TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments. TOPALi v2 provides a Java GUI that submits jobs as web services to HPC clusters or local multi‑core machines, offering model selection, Bayesian and maximum‑likelihood phylogenetic tree estimation, recombination detection, and substitution‑model selection for protein or nucleic‑acid data, with PhyML, RAxML, and MrBayes integrated. TOPALi v2 is freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux, and Solaris. Contact: [e-mail].

Abstract

Abstract Summary: 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 detection methods. The optimal substitution model can be selected for protein or nucleic acid (standard, or protein-coding using a codon position model) data using accurate statistical criteria derived from ML co-estimation of the tree and the substitution model. Phylogenetic software available includes PhyML, RAxML and MrBayes. Availability: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris. Contact: [e-mail]