BioAfrica - Tutorial on the HIV-1 Subtyping Tool

HIV-1 Subtying Tutorial
Examples on How to Interprete the Report:

The report contains three main parts: HIV-1 Subtype analysis, CRFs analysis, and Bootscanning (or Phylogenetic signal) analysis. The first two areas, show the phylogenetic trees constructed with pure subtypes (part one) and CRFs forms (part two). For sequences with more than 1.000 bp a bootscanning analysis is performed and a graphical result displayed, for sequences below 1.000 bp the bootscanning is replaced by phylogenetic signal analysis to determine if the alignment is well suitable for phylogenetic analysis. (More information on methodology used) .

Multiple sequences can be submitted to the REGA HIV-1 subtyping tool.

The batch report (figure1) will be the batch report and contain information on the sequence name, length, assigned subtype and a figure of the HIV-1 genome. Accessing the report link will take the user to a report to each submitted sequence.

The sequence report (figure 2) will be composed of three areas named: sequence assignment, analysis details and phylogenetic analyses.

The Sequence assignment contains information on:

the sequence submitted (name and length),
the classification assignment (subtype, subgroup and bootstrap support),
a graphical representation of the HIV-1 genome showing the genomic region of the query sequence with the start and end positions related to the HXB2 genome,
the motivation of the classification (this is based on the decision tree).

The Phylogenetic analysis section contains:

the phylogenetic tree in PDF and Nexus format,
the log file generated by PAUP (contains info on the model of evolution and its parameters),
the alignment used.

Submit sequences

How to cite

HIV Tutorials

HIV Decision Trees

HIV Subtyping Process

HIV Example Sequences

Developed by: Tulio de Oliveira, Koen Deforche, Sharon Cassol, Andrew Rambaut and Anne-Mieke Vandamme.

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK., the HIV-1 Pathogenesis and Immunotherapeutics Program at University of Pretoria, South Africa, and the REGA Institute at the Katholieke Universiteit Leuven, Belgium.

Funded by the Marie Curie Fellowship, Flanders Bilateral Cooperation Program and the Wellcome Trust (grant # 061238 ).

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