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
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.
by: Tulio de Oliveira, Koen Deforche, Sharon Cassol, Andrew Rambaut and
Developed in cooperation
with the Evolutionary Biology
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.
the Marie Curie Fellowship, Flanders Bilateral Cooperation Program and
Trust (grant # 061238 ).
Revised 16 of June 2005 - Copyright @ BioAfrica