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

Iain Milne; Dominik Lindner; Micha Bayer; Dirk Husmeier; Gráinne Mcguire; David F. Marshall; Frank Wright

doi:10.1093/bioinformatics/btn575

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

Iain Milne, Dominik Lindner, Micha Bayer, Dirk Husmeier, Gráinne Mcguire, David F. Marshall, Frank Wright

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Abstract

UNLABELLED: 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.\n\nAVAILABILITY: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.

Original language	English
Pages (from-to)	126-127
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/btn575
Publication status	Print publication - Jan 2009

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10.1093/bioinformatics/btn575Licence: CC BY-NC

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title = "TOPALi v2: A rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops",

abstract = "UNLABELLED: 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.\n\nAVAILABILITY: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.",

author = "Iain Milne and Dominik Lindner and Micha Bayer and Dirk Husmeier and Gr{\'a}inne Mcguire and Marshall, {David F.} and Frank Wright",

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T1 - TOPALi v2: A rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

AU - Milne, Iain

AU - Lindner, Dominik

AU - Bayer, Micha

AU - Husmeier, Dirk

AU - Mcguire, Gráinne

AU - Marshall, David F.

AU - Wright, Frank

PY - 2009/1

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AB - UNLABELLED: 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.\n\nAVAILABILITY: Freely downloadable from http://www.topali.org for Windows, Mac OS X, Linux and Solaris.

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

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