Evolutionary Biology Group, OxfordBioAfrica

Developers of the Virus Genotyping Tools:

This tool has two publications available. Please cite both papers.

A Standardized Framework for Accurate, High-throughput Genotyping of Recombinant and Non-recombinant Viral Sequences. Alcantara LCJ, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvao-Castro B, Vandamme A-M, and de Oliveira T. (2009) Nucleic Acids Research, 1-9, doi: 10.1093/nar/gkp455     

An Automated Genotyping System for Analysis of HIV-1 and other Microbial Sequences.
de Oliveira T, Deforche K, Cassol S, Salminem M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AMJ, van de Vijver DA, Boucher CA, Camacho R, and Vandamme A-M. (2005) Bioinfomatics; 21 (19), 3797-3800.

The virus genotyping tools are a collaborative project lead by Tulio de Oliveira at the Africa Centre for Health and Population Studies, South Africa. The project involves many Universities and Institutes. These include members of the following groups:

The Zoology Department, University of Oxford, U.K.
-   Oliver Pybus

Institute of Evolutionary Biology, University of Edinburgh, U.K.
-   Andrew Rambaut

Prof. Anne-Mieke Vandamme and Prof. Marc Van Ranst, REGA Institute, Katholieke Universiteit Leuven, Belgium
-    Ana Abecasis
-    Koen Deforche
-    Annabel Rector
-    Joke Snoeck
-    Sonia Van Dooren
-    Marc Van Ranst
-    Anne-Mieke Vandamme

Dr  Ricardo Camacho, Virology Laboratory, Hospital Egas Moniz,  Portugal
-    Ricardo Camacho

Prof. Sharon Cassol,  HIV-1 Immune Pathogenesis and Therapeutics Research Program,  University of Pretoria, South Africa.
-    Sharon Cassol
-    Taryn Page

Prof. Bernardo Galvao-Castro, Laboratorio Avancado de Saude Publica (LASP) CPqGM/FIOCRUZ, Brazil
-    Luiz Carlos Alcantara
-    Bernardo Galvao-Castro
-    Ramon Moreau

Prof. Marco Salemi, Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, USA
-    Marco Salemi

Prof. Arnaldo Zaha, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil
-    Sabrina Matos Almeida
-    Arnaldo Zaha


The following groups also mirror the virus genotyping tools:
  • Prof. Robert Shafer, Stanford University, USA.



Funded by the Marie Curie Fellowship, Flanders Bilateral Cooperation Program,Wellcome Trust and Royal Society, UK.


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For questions, suggestions or problems please contact:  Dr. Tulio de Oliveira.