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

By Iain Milne, Dominik Lindner, M. Bayer, Dirk Husmeier, Gráinne McGuire, D. Marshall, F. Wright. Bioinform., 2008

650 citations recorded by the source corpus.

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: iain.milne@scri.ac.uk

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dda8b7071651cc4e51f67e22ed43ab40654e5ef3

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Citations in the corpus

ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution (2010, methodology): “In addition, some model selection capabilities have been added to more general phylogenetic programs like HYPHY [12], Treefinder [6] or TOPALi [11].”
Characterization of Pseudomonas syringae pv. actinidiae (Psa) isolated from France and assignment of Psa biovar 4 to a de novo pathovar: Pseudomonas syringae pv. actinidifoliorum pv. nov. (2015, methodology): “Phylogenetic trees and bootstrap values were obtained for each gene and the concatenated data by the PHYML (Guindon et al., 2010) method using TOPALI v. 2.5 (Milne et al., 2009; available at http://www.topali. org/).”