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Oxford HCV Subtyping Tool Tutorial

Multiple sequences can be submitted to the Oxford HCV 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 HCV 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 HCV genome showing the genomic region of the query sequence with the start and end positions related to the 1A.COLONEL 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
HCV Tutorials
HCV Decision Trees
HCV Subtyping Process
HCV Example Sequences
Contact us

Developed by: Tulio de Oliveira, Marco Salemi, Oliver Pybus, Sabrina Almeida,  Andrew Rambaut.

Developed by the Evolutionary Biology Group at University of Oxford, UK. Department of Pathology, Immunology & Laboratory Medicine, University of Florida, Gainesville, USA. Biotechnology department, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil.

Funded by the Marie Curie Fellowship, Royal Society and Wellcome Trus, UK.

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