Bioinformatics Software and Tools

These are some of the bioinformatics software and tools which we develop. All of the tools are open source and free available on this website.



Bioinformatics Tools
Description


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


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

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.

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.


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.

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

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

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

PAUP* scripts resources 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.


Revised 15 of May 2008 - Tulio de Oliveira.