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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

About the Authors

Sergei L. Kosakovsky Pond
Department of Medicine, University of California San Diego, La Jolla, California, United States of America
David Posada
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
Eric Stawiski, Colombe Chappey
Monogram Biosciences, South San Francisco, California, United States of America
Art F.Y. Poon, Simon D.W. Frost
Department of Pathology, University of California San Diego, La Jolla, California, United States of America
Gareth Hughes
Health Protection Agency East of England Regional Epidemiology Unit, Cambridge, United Kingdom
Esther Fearnhill
Medical Research Council Clinical Trials Unit, London, United Kingdom
Mike B. Gravenor
School of Medicine, University of Swansea, Swansea, United Kingdom
Andrew J. Leigh Brown
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
Simon D.W. Frost
Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

Corresponding Author

Email: spond@ucsd.edu

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: SLKP DP AJLB SDWF. Performed the experiments: SLKP. Analyzed the data: SLKP DP ES GH. Contributed reagents/materials/analysis tools: SLKP DP ES CC AFYP GH EF MBG SDWF. Wrote the paper: SLKP DP AFYP SDWF.