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Research Article

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

  • Sergei L. Kosakovsky Pond mail,

    spond@ucsd.edu

    Affiliation: Department of Medicine, University of California San Diego, La Jolla, California, United States of America

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  • David Posada,

    Affiliation: Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain

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  • Eric Stawiski,

    Affiliation: Monogram Biosciences, South San Francisco, California, United States of America

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  • Colombe Chappey,

    Affiliation: Monogram Biosciences, South San Francisco, California, United States of America

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  • Art F.Y. Poon,

    Affiliation: Department of Pathology, University of California San Diego, La Jolla, California, United States of America

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  • Gareth Hughes,

    Affiliation: Health Protection Agency East of England Regional Epidemiology Unit, Cambridge, United Kingdom

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  • Esther Fearnhill,

    Affiliation: Medical Research Council Clinical Trials Unit, London, United Kingdom

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  • Mike B. Gravenor,

    Affiliation: School of Medicine, University of Swansea, Swansea, United Kingdom

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  • Andrew J. Leigh Brown,

    Affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

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  • Simon D.W. Frost

    Affiliations: Department of Pathology, University of California San Diego, La Jolla, California, United States of America, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

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  • Published: November 26, 2009
  • DOI: 10.1371/journal.pcbi.1000581

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