论文信息 - ProtTest 3: fast selection of best-fit models of protein evolution

ProtTest 3: fast selection of best-fit models of protein evolution

UNLABELLED We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities. AVAILABILITY ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked to a Mercurial repository at Bitbucket (https://bitbucket.org/). CONTACT dposada@uvigo.es SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[2] Michael Nilges,et al. ISD: a software package for Bayesian NMR structure calculation , 2008, Bioinform..

[3] Mark Baker,et al. Nested parallelism for multi-core HPC systems using Java , 2009, J. Parallel Distributed Comput..

[4] L. Dagum,et al. OpenMP: an industry standard API for shared-memory programming , 1998 .

[5] Florentino Fernández Riverola,et al. ALTER: program-oriented conversion of DNA and protein alignments , 2010, Nucleic Acids Res..

[6] James E. Byers,et al. MODEL SELECTION IN PHYLOGENETICS , 2005 .

[7] Korbinian Strimmer,et al. PAL: an object-oriented programming library for molecular evolution and phylogenetics , 2001, Bioinform..

[8] D. Posada,et al. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. , 2004, Systematic biology.

[9] David Posada,et al. ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..