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A novel methodology for large-scale phylogeny partition

Author

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  • Mattia C.F. Prosperi

    (Clinic of Infectious Diseases, Catholic University of the Sacred Heart
    Immunology and Laboratory Medicine, College of Medicine, Emerging pathogens Institute, University of Florida, PO BOX 103633, Gainesville, Florida, USA.
    Emerging Pathogens Institute, University of Florida)

  • Massimo Ciccozzi

    (Istituto Superiore di Sanità)

  • Iuri Fanti

    (Clinic of Infectious Diseases, Catholic University of the Sacred Heart)

  • Francesco Saladini

    (Section of Microbiology, University of Siena)

  • Monica Pecorari

    (Modena Hospital)

  • Vanni Borghi

    (Infectious Diseases Clinic, Modena Hospital)

  • Simona Di Giambenedetto

    (Clinic of Infectious Diseases, Catholic University of the Sacred Heart)

  • Bianca Bruzzone

    (Hygiene Unit, S. Martino Hospital)

  • Amedeo Capetti

    (L. Sacco Hospital, University of Milan)

  • Angela Vivarelli

    (Infectious Diseases Clinic, Pistoia Hospital)

  • Stefano Rusconi

    (Section of Infectious Diseases and Immunopathology, L. Sacco Hospital, University of Milan)

  • Maria Carla Re

    (Section of Microbiology, University of Bologna)

  • Maria Rita Gismondo

    (Microbiology Laboratory, L. Sacco Hospital, University of Milan)

  • Laura Sighinolfi

    (S. Anna Hospital)

  • Rebecca R. Gray

    (Immunology and Laboratory Medicine, College of Medicine, Emerging pathogens Institute, University of Florida, PO BOX 103633, Gainesville, Florida, USA.
    Emerging Pathogens Institute, University of Florida)

  • Marco Salemi

    (Immunology and Laboratory Medicine, College of Medicine, Emerging pathogens Institute, University of Florida, PO BOX 103633, Gainesville, Florida, USA.
    Emerging Pathogens Institute, University of Florida)

  • Maurizio Zazzi

    (Section of Microbiology, University of Siena)

  • Andrea De Luca

    (Clinic of Infectious Diseases, Catholic University of the Sacred Heart
    Infectious Diseases Unit II, University Hospital of Siena)

Abstract

Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data.

Suggested Citation

  • Mattia C.F. Prosperi & Massimo Ciccozzi & Iuri Fanti & Francesco Saladini & Monica Pecorari & Vanni Borghi & Simona Di Giambenedetto & Bianca Bruzzone & Amedeo Capetti & Angela Vivarelli & Stefano Rus, 2011. "A novel methodology for large-scale phylogeny partition," Nature Communications, Nature, vol. 2(1), pages 1-10, September.
    • Handle: RePEc:nat:natcom:v:2:y:2011:i:1:d:10.1038_ncomms1325
    DOI: 10.1038/ncomms1325
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