REGA HIV Subtyping Tool pipeline

REGA HIV Subtyping Tool specifications

Information


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 Yes

Taxon


  • Viruses
    • Human immunodeficiency virus

Maintainers


  • person_outline Tulio De Oliveira <>
  • person_outline Tulio De Oliveira <>
  • person_outline Tulio de Oliveira <>

Additional information


http://dbpartners.stanford.edu:8080/RegaSubtyping/stanford-hiv/typingtool

Publications for REGA HIV Subtyping Tool

REGA HIV Subtyping Tool citation

2014
PMCID: 4053352

[…] and for which the sampling year was known, were downloaded from the los alamos hiv sequence database (www.hiv.lanl.gov) by august 2013. the subtype assignment of all sequences was confirmed by: rega hiv subtyping tool v.2 [33], maximum likelihood (ml) phylogenetic analysis, and bootscanning analysis. a ml phylogeny with hiv-1 group m subtype reference sequences was constructed […]

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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