Very large phylogenies are being built today in order to study virus evolution, trace the origin of epidemics, establish the mode of transmission, and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance.

We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in very low computing times.

There is three ways to compute a PhyloType analysis. The first one is the use of the web interface (see the "Interface" link above), the second one is to use a standalone module to download and the third way is to use a "batchmode" module (for massive PhyloType analyses, without a graphical user interface).

(see the News section below for more details)

July 15 2014. PhyloType batchmodule (PBM), version 07
  • PhyloType PBM7.0 LINUX
  • PhyloType PBM7.0 OSX
  • PhyloType PBM7.0 WINDOWS (32)

  • July 15 2014. PhyloType standalone (PST), version 07
  • PhyloType PST7.0 LINUX
  • PhyloType PST7.0 OSX
  • PhyloType PST7.0 WINDOWS (32)

  • If you use this site, please cite:

    Searching for Virus Phylotypes
    Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O.
    Bioinformatics (2013) Volume 29, Issue 5Pp. 561-570.

    Questions and comments much welcome !,,
    François Chevenet
    Olivier Gascuel
    Tulio de Oliveira

  • July 15 2014.PhyloType version 07.
    • web, pst, pbm : Persistence criteria revisited
    • pbm : new parameters file (new output : tree with ancestral annotations and node IDs (in place of support values))
  • May 28 2014.PhyloType standalone module (PST) and batchmodule (PBM) version 04

  • HIVphyML project (NRF South Africa and CNRS France)
  • PhyloSpace project (ANR 6ème Extinction)
  • Wellcome Trust (grant 082384/Z/07/Z)
  • NUMEV Developpement de la plateforme ATGC