Bioinformatics Software Applications, Sequence Databases & Online Tools

These are some of the bioinformatics software applications, online databases and and tools developed by our research group in South Africa. All of the tools are open-source and freely available online. Our Bioinformatics servers tools and databases are hosted in Linux servers a the South African Medical Research Council, Cape Town, South Africa.Please follow link below.



Dengue, Zika and Chikungunya viruses typing tool: A phylogenetic algorithm for accurate identification of Dengue, Zika and Chikungunya viruses species and genotypes.



SPOTLIGHT


High-Throughput Genomics Facility at Nelson R Mandela School of Medicine, UKZN in collaboration with Africa Centre for Health and Population Studies


BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools


Rega HIV Subtyping Tool V3 - Belgium mirror



TYPING TOOLS

2016-08-21
Version: 3


REGA HIV Subtyping Tool V3 - South African mirror

This tool is designed to use phylogenetic methods in order to identify the HIV-1 subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).


2016-08-20
Version: 1


Zika Typing Tool

This is the first version of the Zika typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.


2016-08-20
Version: 1


Arbovirus Typing Tool

This is the first version of our Arbovirus typing tool for Chikungunya, Dengue, Yellow Fever and Zika


2016-08-20
Version: 1


Chikungunya Typing Tool

This is the first version of the Chikungunya typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.


2016-08-20
Version: 1


Yellow Fever Virus Typing Tool

This is the first version of the Yellow Fever typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.


2015-11-06
Version: 1


Dengue Virus Typing Tool

This is a beta version of our Dengue Virus Typing tool. For the mean time, this tool should be used for evaluation only. Please send feedback to Tulio de Oliveira.


2015-11-05
Version: 2


HTLV 1 & 2 Typing Tool

This is a beta version of our HTLV 1 & 2 Typing tool. For the mean time, this tool should be used for evaluation only. Please send feedback to Tulio de Oliveira.


2015-11-05
Version: 2


HCV Typing Tool

This is a beta version of our HCV Typing tool. For the mean time, this tool should be used for evaluation only. Please send feedback to Tulio de Oliveira.


2014-04-01
Version: 3


Rega HIV Subtyping Tool V3 - Belgium mirror

This tool is designed to use phylogenetic methods in order to identify the HIV-1 subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).


2014-03-31
Version: 3


REGA HIV Subtyping Tool V3 - Stanford Mirror

Phylogenetic tool to identify the HIV-1 subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).


2014-03-12
Version: 2


REGA HIV Subtyping Tool V2 - South African mirror

This tool is designed to use phylogenetic methods in order to identify the HIV-1 subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods. The version 2 contains CRFs (CRF01_AE to CRF12_BF).


2014-02-10
Version: 2


Oxford HBV Subtyping Tool V2 - South African mirror

Phylogenetic tool to identify the Hepatitis B Virus (HBV) subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods.


2014-02-10
Version: 2


HHV8 Automated Subtyping Tool

Phylogenetic tool to identify the Human Herpesvirus 8 (HHV-8) subtypes and recombinants. Query sequences are analysed against the complete K1 reference sequences for HHV8 subtypes A, A5, B, C, D and E.


2014-02-09
Version: 2


Human Papillomavirus Subtyping Tool

Phylogenetic tool to identify the Human Papillomavirus (HPV) subtypes and species. Query sequences are analysed against the complete L1 reference sequences for HPV and involve the construction of a phylogenetic tree using HKY distance method with gamma distribution in PAUP* software. The HHV8 subtypes and sub-groups are identified.


2009-01-10
Version: 2


OXFORD HCV Subtyping Tool

Phylogenetic subtyping tool for HCV


2009-01-09
Version: 2


LASP HTLV-1 Subtyping Tool

Phylogenetic subtyping tool for HTLV-1




DATABASES

2015-01-14
Version: 2


SATuRN RegaDB Online tool

This database is a free password-protected open source database available. Access to the highly curated data sets is through applications that are reviewed by the SATuRN executive committee


2010-12-10
Version: 1


Southern African Mirror of the Stanford HIV Drug Resistance Database (HIVDB)

A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance


2009-10-10
Version: 1


RNA Virus Database

The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for all known species of RNA virus.




ONLINE TOOLS

2013-03-31
Version: 1


Searching for Virus Phylotypes: Online Tool

Online web interface that provides an interface to identify phylotypes and allows for exploratory analyses of very large data sets.


2008-12-01
Version: 1


Blast Servers

Blast using local databases at our servers. It includes HIV Genbank, Subtype Reference Dataset and HXB2 reference sequence databases


2008-12-01
Version: 1


BlastAlign

Online web version for BlastAlign software application


2007-01-07
Version: 1


HIV Quality Analysis Tool

Tool to determine quality and contamination of sequences using local Blast


2007-01-06
Version: 1


HIV Epitope Analysis Tool

Online tools for searching for epitopes using local Blast




SCIENTIFIC RESOURCES

2015-04-14
Version: 1


High-Throughput Genomics Facility at Nelson R Mandela School of Medicine, UKZN in collaboration with Africa Centre for Health and Population Studies

The aim of the Genomics Facility is to setup one of the world's most advanced and respected genetic sequencing systems to UKZN in order to enable and support world-class genomics research in Africa. Our objective is to use NextGen sequencing and bioinformatics to answer scientific questions that are of local, national and international importance. Collaborators are welcome to apply for projects to generate HIV, TB, 16S and host genomic data.


2015-01-14
Version: 1


BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools

Contains information about each HIV-1 gene product in regard to expression, functional activities, and interactions with viral and host macromolecules


2003-01-09
Version: 1


PAUP* Scripts

Set of PAUP* scripts to contruct maximum likelihood trees




SOFTWARE DOWNLOAD

2015-01-01
Version: 1


Phylotype standalone interface

Download phylotype standard alone interfaces for Mac OS X, Linux and Windows system. A batch and command line version for large analysis is also available.


2013-02-01
Version: 1


RegaDB: Community-driven data management and analysis for infectious diseases

RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.


2003-12-01
Version: 1


GDE Linux

Genetic Data Environment (GDE) interface for HIV-1 coded in Linux Operation System





Page design updated by Tulio de Oliveira, 2011