Web tools
- QUALITY
A program that is a variant of the Minimum χ2 (MC) method for limiting dilution assays.
It allows the user to specify the probabilities of a false negative and false positive PCR
(it is also a tool for the quantitation of ampliable viral templates, i.e., viral load
under the conditions of your assay). The program is available either as a java applet
that can be run via the web or as a program that can be downloaded and run locally.
- PSSM
A scoring tool that allows users to analyze V3 loop coreceptor motifs.
- ViroBLAST
A BLAST web server that allows users to search multiple sequence databases including public and local databases.
- DIVER
A web interface to analyze sequence divergence and diversity.
- InSites
A web interface to detect informative sites in a set of aligned nucleotide or amino acid sequences.
- EpitopeDB
A web database to store, retrieve and analyze HIV immunology data (ELISpot, HLA, etc.).
- PrimerDB
A web database to store, search and retrieve lab used HIV primers.
- LiteraTracker
A web service to track literatures.
- COTree
A web interface that re-roots a newick tree at the least squares point (COT).
- rdvg
A test for the detection of latent reservoirs.
- idvg
A test for the detection of continued viral replication under antiviral therapies.
- DistParser
A tool to pull branch lengths from newick tree and returns divergence and diversity.
- JitterCalc
An Excel spreadsheet that jitters points with identical (x, y) values.
- PAUP* Diversity Matrix Formatter A tool to reformat diagonal distance matrices into columnar output
|