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REGA HIV Subtyping Tool specifications


Unique identifier OMICS_06320
Name REGA HIV Subtyping Tool
Alternative names REGA HIV-1 Subtyping Tool, REGA HIV-2 Subtyping Tool
Interface Web user interface
Restrictions to use None
Input data Some sequences.
Input format FASTA
Output data A report containing three main parts: HIV-1 Subtype analysis, CRFs analysis, and Bootscanning (or Phylogenetic signal) analysis.
Output format (CSV,XML)+(PDF,Nexus)
Programming languages Java, PHP
Computer skills Basic
Version 2.0
Stability Stable
Maintained No


  • Viruses
    • Human immunodeficiency virus 1
    • Human immunodeficiency virus 2


This tool is not available anymore.

Additional information

Publications for REGA HIV Subtyping Tool

REGA HIV Subtyping Tool citations


Pretreatment drug resistance in a large countrywide Ethiopian HIV 1C cohort: a comparison of Sanger and high throughput sequencing

Sci Rep
PMCID: 5954158
PMID: 29765082
DOI: 10.1038/s41598-018-25888-6

[…] Subtyping was done by Recombinant Identification Program (, REGA HIV Subtyping Tool v3, ( and COMET HIV-1 ( Maximum likelihood phylogenetic analysis was pe […]


Novel HLA class I associations with HIV 1 control in a unique genetically admixed population

Sci Rep
PMCID: 5904102
PMID: 29666450
DOI: 10.1038/s41598-018-23849-7
call_split See protocol

[…] HIV subtypes were determined using REGA HIV Subtyping Tool (3.0) ( and confirmed with the Recombination Identification Program (RIP, […]


Brazilian network for HIV Drug Resistance Surveillance (HIV‐BresNet): a survey of treatment‐naive individuals

PMCID: 5835841
PMID: 29504269
DOI: 10.1002/jia2.25032

[…] The HIV subtype characterization was evaluated for the 1568 analysed pol sequences using the REGA HIV‐1 subtyping tool , and HIVdb Program . With the exception of the south, the subtype B (n = 1045, 66.8%) remains the most prevalent in Brazil, followed by subtypes C (n = 223, 14.2%) and F (n […]


Weaker HLA Footprints on HIV in the Unique and Highly Genetically Admixed Host Population of Mexico

J Virol
PMCID: 5752930
PMID: 29093100
DOI: 10.1128/JVI.01128-17
call_split See protocol

[…] HIV subtypes were determined using the REGA HIV subtyping tool (3.0) ( and confirmed with the Recombination Identification Program (RIP; […]


HIV 1 envelope sequence based diversity measures for identifying recent infections

PLoS One
PMCID: 5746209
PMID: 29284009
DOI: 10.1371/journal.pone.0189999
call_split See protocol

[…] We used two HIV subtyping tools to determine a consensus HIV subtype. The Rega HIV Subtyping Tool V3 [] ( and, Confirmation with the NCBI HIV Subtyping tool [] ( […]


Assessment of HIV molecular surveillance capacity in the European Union, 2016

PMCID: 5727594
PMID: 29233253
DOI: 10.2807/1560-7917.ES.2017.22.49.17-00269

[…] All countries used population sequence analysis to generate their sequence data. Three countries also reported using next-generation sequencing (NGS) analysis to generate their HIV sequence data. The Rega HIV subtyping tool (n = 6 countries) and the Stanford HIV Drug resistance database (n = 3 countries) were the most widely reported tools for subtype analysis. There was little difference among co […]


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REGA HIV Subtyping Tool institution(s)
Laboratorio Avancado de Saude Publica, Centro de Pesquisas Goncalo Moniz, Fundacao Oswaldo Cruz, Brazil; MRC Unit for Inflammation and Immunity, Department of Immunology, University of Pretoria and Tshwane Academic Division of the National Health Laboratory Service, Pretoria, South Africa; Laboratory for Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, Rotselaar, Belgium; Department of Zoology, University of Oxford, UK; Africa Centre for Health and Population Studies, University of KwaZulu-Natal, South Africa
REGA HIV Subtyping Tool funding source(s)
Supported by Katholieke Universiteit Leuven (grant OT/04/43); Belgian Fonds voor Wetenschappelijk Onderzoek (F.W.O. nr G.0266.04); Virolab project (EU IST STREP Project 027446); the Wellcome Trust (082384/ Z/07/Z) and European Union (SANTE 2007 147-790); the Africa Centre for Health and Population Studies; the European Union (SANTE 2007 147-790) and NRF, South Africa. The Royal Society.

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