Bioafrica home page Laboratory for Clinical and Evolutionary Virology home page

LASP HTLV-1 Subtyping Tool Tutorial

Multiple sequences can be submitted to the LASP HTLV-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 HTLV-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 HTLV-1 genome showing the genomic region of the query sequence with the start and end positions related to the ATK1 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
HTLV Tutorials
HTLV Decision Trees
HTLV Subtyping Process
HTLV Example Sequences
Contact us

Developed by: Luiz Carlos J Alcantara,  Sonia Van Dooren, Anne-Mieke Vandamme, Bernardo Galvao-Castro, Tulio de Oliveira.

Developed in cooperation with the Evolutionary Biology Group at University of Oxford, UK, the REGA Institute at the Katholieke Universiteit Leuven, Belgium and the Laboratorio Avancado de Saude Publica (LASP) CPqGM/FIOCRUZ, Brazil.

Funded by the Marie Curie Fellowship, Flanders Bilateral Cooperation Program, PN-DST/AIDS (Ministry of Health) and FAPESB, Brazil.

For HTLV-1 subtyping questions please contact Dr Luiz Alcantara,
Suggestions or problems on the program please contact:  Dr Tulio de Oliveira.