Title: Searching for Virus Phylotypes
Authors: Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O.
Journal: Bioinformatics,29 (5):561-570 (2013)


Motivation: 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.

Results: 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, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is very large, containing more than 3,000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones.

Availability: This method and companion tools are implemented in an interactive Web interface (, which provides a wide choice of graphical views and output formats, and allows for exploratory analyses of very large data sets.

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

Summary PowerPoint Presentation

Chevenet F, Jung M, Peeters M, <a href='people.php?fullName=de Oliveira T'>de Oliveira T</a>, Gascuel O. Searching for Virus Phylotypes .Bioinformatics,29 (5):561-570 (2013)

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Media Coverage of this Publication:

UKZN Research Centres Collaborate to Celebrate World AIDS Day - UKZN - 2012-11-29

The Health Economics and HIV and AIDS Research Division (HEARD) in collaboration with CAPRISA, SATuRN/Africa Centre and the University of KwaZulu-Natal Press hosted Getting to Zero: Showcasing KZN Research on HIV and AIDS on 14 November at the KZNSA Gallery.

KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).

Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira