title: TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops.
abstract: 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.
  
  
  BACKGROUND
  Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.
authors.affiliation: Scottish Crop Research Institute, Invergowrie, Dundee, UK. iain.milne@scri.ac.uk
authors.forename: Iain
authors.initials: I
authors.lastname: Milne
authors.forename: Dominik
authors.initials: D
authors.lastname: Lindner
authors.forename: Micha
authors.initials: M
authors.lastname: Bayer
authors.forename: Dirk
authors.initials: D
authors.lastname: Husmeier
authors.forename: Gráinne
authors.initials: G
authors.lastname: McGuire
authors.forename: David F
authors.initials: DF
authors.lastname: Marshall
authors.forename: Frank
authors.initials: F
authors.lastname: Wright
mesh_terms: D003062:Codon / Q000235:genetics; D003196:Computer Graphics; D003201:Computers; D019143:Evolution, Molecular; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment / Q000295:instrumentation*; D014584:User-Computer Interface
chemical_list: D003062:Codon