Journal
BIOINFORMATICS
Volume 25, Issue 1, Pages 126-127Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btn575
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Funding
- UK BBSRC/EPSRC Bioinformatics/E-science Initiative [BBSB16615]
- Scottish Government
- Scottish Funding Council
- Scottish Enterprise
- Biotechnology and Biological Sciences Research Council [BBS/B/16615] Funding Source: researchfish
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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 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.
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