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Oxford HCV Subtyping Tool Decision Tree




Rule 1: Subtype Assigned
Subtype assigned based on sequence > 800 bps, clustering with a pure subtype with bootstrap > 70% without recombination in the bootscan.

Rule 2: check the bootscan
Subtype unassigned based on sequence > 800bp, clustering with a pure subtype with bootstrap >70 %, with detection of recombination in the pure subtype bootscan.


Rule 3: check the report
Subtype unassigned based on sequence > 800bp, do not clustering with a pure subtype with bootstrap >70 %, with no detection of recombination in the pure subtype bootscan.

Rule 4: check the bootscan
Subtype unassigned based on sequence > 800bp, do not clustering with a pure subtype with bootstrap > 70 %, with detection of recombination in the pure subtype bootscan.


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Rule 5: Pure
Subtype assigned based on sequence < 800bp, clustering with inside a HCV subtype with bootstrap > 70%.

Rule 5: check the report
Subtype assigned based on sequence < 800bp, clustering with outside a HCV subtype with bootstrap > 70%.

Rule 6: check the report
Subtype unassigned based on sequence < 800bp, do not clustering with a pure subtype with bootstrap >70 %.


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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.