Bioinformatics Software and Tools

These are some of the bioinformatics software applications and tools developed in our research group. All of the tools are open-source and freely available on this website.We are based at the Africa Centre for Health and Population Studies, the Nelson R Mandela School of Medicine, University of KwaZulu-Natal, South Africa and the HIV-1 Mucosal Pathogenesis and Treatment Program, Department of Immunology, University of Pretoria, South Africa.

Picture Description


Blast Servers - for HIV, HCV and HBV numbering positioning, fast subtyping, alignment, search private and public databases.


BlastAlign - is a program that uses blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align.


GDE Linux - Genetic Data Environment for Linux and Mac OS X.


HIV Epitope Analysis Tool - This tool is designed to determine the similarities and mutations on epitope sequences. The sequence will be searched against the HIV-1 subtypes A, B and C consensus and ancestral sequences.


HIV Quality Analysis Tool - is designed to determine the quality of a specific HIV sequence. Sequence translational problems are identified using complete genome and the proteome of the HIV-1 reference sequence HXB2.


LASP HTLV-1 Subtyping Tool - uses phylogenetic methods to identify the subtype and sub-group of HTLV-1 sequences.


PAUP* Scripts - Contains a number of PAUP* scripts for different models of substitutions (F81, TrN, HKY, TVM and GTR). Scripts can be used to construct fine maximum likelihood and neighbour-joining phylogenetic trees.


REGA HCV Subtyping Tool - uses phylogenetic methods to identify the genotype and subtype of query sequences.


REGA HIV Subtyping Tool - uses phylogenetic methods to identify the subtype or CRF of query sequences.


Viral Genotyping Tools - link to subtyping HHV8, HTLV-1 and HPV. This tool uses phylogenetic methods to identify the subtype of a query sequence.


Page design updated by Tulio de Oliveira, 2011