Bioinformatics Software and ToolsThese 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. |
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Blast Servers for HIV, HCV and HBV numbering positioning, fast subtyping, alignment, search private and public databases. |
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BlastAlign is a program that uses blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align. |
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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. |
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GDE Linux - Genetic Data Environment for Linux and Mac OS X. |
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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. |
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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. |
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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. |
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REGA HCV Subtyping Tool uses phylogenetic methods to identify the genotype and subtype of query sequences. |
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REGA HIV Subtyping Tool uses phylogenetic methods to identify the subtype or CRF of query sequences. |
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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. |