University of Cambridge > > Isaac Newton Institute Seminar Series > Fast exploratory analysis of very large phylogenies; application to HIV epidemic

Fast exploratory analysis of very large phylogenies; application to HIV epidemic

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If you have a question about this talk, please contact Mustapha Amrani.


Large phylogenies are being built today for a number of life domains, typically comprising several thousands of taxa. However, tools are lacking to quickly analyze these phylogenies and combine them with extrinsic traits (e.g. geographic location), seeking to decipher the evolutionary history of studied taxa, not only their shared ancestry, but also their displacements on the surface of earth, their dates of appearance and their adaptations to various ecological conditions. I will present two such tools, with applications to virus epidemics, but based on general principles and ideas and applicable to a wide range of biological questions. I will first discuss distance-based approaches to estimate rates and dates, and present a new fast least-squares algorithmic scheme to estimate evolutionary rates from heterochronous data where taxa are sampled at different time points. Then, I will present an interactive Web interface ( to extract taxon groups of special i nterest, by combining extrinsic traits, ancestral trait reconstruction, and combinatorial, numerical and statistical criteria. Several applications to HIV will be discussed.

  • Collaboration with Matthieu Jung (LIRMM-CNRS and IRD , Montpellier, France)
  • Collaboration with Franois Chevenet (LIRMM-CNRS and IRD , Montpellier, France) and Tulio de Oliveira (Africa Centre for Health and Population Studies University of KwaZulu-Natal, South Africa)
  • Collaboration with Tulio de Oliveira and Martine Peeters (IRD, Montpellier, France)

This talk is part of the Isaac Newton Institute Seminar Series series.

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