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BioAfrica specifications


Unique identifier OMICS_20921
Name BioAfrica
Alternative name BioAfrica HIV-1 Proteomics Resource
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes


  • person_outline Tulio De Oliveira
  • person_outline Tulio De Oliveira

Publication for BioAfrica

BioAfrica citations


Co circulation and simultaneous co infection of dengue, chikungunya, and zika viruses in patients with febrile syndrome at the Colombian Venezuelan border

BMC Infect Dis
PMCID: 5791178
PMID: 29382300
DOI: 10.1186/s12879-018-2976-1

[…] s obtained were compared with various prototype strains of each of these viruses using BLAST and the on-line tool, Dengue, Zika & Chikungunya Viruses Typing Tool Version 0.9 – Alpha (available at […]


Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil

Sci Rep
PMCID: 5680240
PMID: 29123142
DOI: 10.1038/s41598-017-15152-8

[…] s were removed from subsequent analysis to avoid introducing biases in evolutionary rate estimates. DENV types were classified using the Dengue, Zika and Chikungunya Viruses Typing Tool v.0.9 ( […]


Characterization of Nucleoside Reverse Transcriptase Inhibitor Associated Mutations in the RNase H Region of HIV 1 Subtype C Infected Individuals

PMCID: 5707537
PMID: 29117130
DOI: 10.3390/v9110330
call_split See protocol

[…] nsed software programs ( and aligned against HXB2 reference strain []. The alignment was manually edited using the Genetic Data Environment v2.2 ( HIV-1 subtype was determined by the REGA HIV-1 subtyping tool version 3 [,]. A maximum likelihood phylogenetic tree was built with PhyML using the GTR substitutio […]


Expanding HIV 1 subtype B transmission networks among men who have sex with men in Poland

PLoS One
PMCID: 5325290
PMID: 28234955
DOI: 10.1371/journal.pone.0172473

[…] om the start of HXB2 genome: positions 2253 to 3525. Identification of subtype B was performed based on the partial pol sequences using two methods: on-line software (REGA genotyping 2.0 tool; and phylogenetic analyses using maximum likelihood (ML) method under the GTR+γ model with approximate likelihood ratio test (aLRT) (online PHY […]


Spatiotemporal dynamics of HIV 1 transmission in France (1999–2014) and impact of targeted prevention strategies

PMCID: 5322782
PMID: 28222757
DOI: 10.1186/s12977-017-0339-4

[…] HIV-1 subtypes were determined uploading sequences individually into the REGA HIV-1 automated Subtyping Tool version 2.0 ( and confirmed by in-house phylogenetic analysis.The age of the most recent common ancestor (TMRCA, years) and the ancestral geographic movements wer […]


The PTAP sequence duplication in HIV 1 subtype C Gag p6 in drug naive subjects of India and South Africa

BMC Infect Dis
PMCID: 5259826
PMID: 28118816
DOI: 10.1186/s12879-017-2184-4
call_split See protocol

[…] contained a total of 1,632 nucleic acid positions. Additionally, genetic subtype characterization of the gag sequences was performed using the REGA HIV-1 Subtyping Tool version 2.0, available at the BioAfrica site ( and the recombinant identification tool available at the Los Alamos HIV Sequence Database ( Every indiv […]


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BioAfrica institution(s)
Africa Centre for Population Health, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Division of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa; Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
BioAfrica funding source(s)
Supported by the Swiss South African Joint Research Programme (SSJRP) research grant entitled "Swiss Prot / South Africa: Protein Bioinformatics Resource Development for Important Health- related Pathogens, the Swiss Federal Government through the State Secretariat for Education, Research and Innovation, Flagship grant from the Medical Research Council (MRC) of the Republic of South Africa (MRCRFA-UFSP-01-2013/UKZN HIVEPI) the Wellcome Trust (082384/Z/07/Z) and a Royal Society Newton Advanced Fellowship.

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