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.



Bioinformatics Tools
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.


CPR - Calibrated Population Resistance Tool

CPR - Calibrated Population Resistance Tool HIV-1 drug resistance tool developed by Dr. Robert Gifford and colleagues in the Stanford HIV Drug Resistance Database to calculate the prevalence of HIV drug resistance in population sequences.

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

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.
Virus Genotyping Tools
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 last updated by Tulio de Oliveira.