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Tutorial on the REGA HPV Automated Subtying Tool 

Up to 1000 sequences can be submitted at once to the BioAfrica HPV 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 HPV 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 HPV genome showing the genomic region of the query sequence with the start and end positions related to the HPV1 reference 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
HPV Tutorials
HPV Decision Trees
HPV Subtyping Process
HPV Example Sequences
Contact us

Developed by: Annabel Rector, Marc Van Ranst, Andrew Rambaut, and Tulio de Oliveira.

Developed in collaboration between the Africa Centre for Health and Population Studies bioinformatics group, UKZN, South Africa and the the REGA Institute at the Katholieke Universiteit Leuven, Belgium.

Funded by the Marie Curie Fellowship, Flemish Fund for Scientific Research (Fonds voor Wetenschappelijk Onderzoek, FWO) grant G.0513.06 and by a postdoctoral fellowship of the Research Fund K.U.Leuven

Suggestions or problems on the program please contact:  Dr Tulio de Oliveira.