BIOTOOLS SPOTLIGHT






KRISP BIOTOOLS INTRODUCTION:

KRISP host many of the tools that were developed in Bioafrica.net (Prof. Tulio de Oliveira old group website). The great majority of our tools are freely and openly accessible. In addition, we also provide a linux cluster so the tools can be used free of charge.


Blast Servers

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



BlastAlign

Online web version for BlastAlign software application



Booster: a new bootstrap method for construction of large trees

A new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual 'transfer' distance rather than the binary presence or absence index used in Felsenstein's original version. The resulting supports are higher and do not induce falsely supported branches.



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.



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.



Genome Detective

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



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.



HIV Quality Analysis Tool

Tool to determine quality and contamination of sequences using local Blast



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



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.



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.



Phylotype Online Tool

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



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).



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).



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.



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



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



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.



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.



KRISP High-Processing Computer Servers have > 300 Bioinformatics Software Applications

Genome Detective