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.
A scoring tool that allows users to analyze V3 loop coreceptor motifs.
A BLAST web server that allows users to search multiple sequence databases including public and local databases.
A web server to analyze phylogenies, sequence divergence, diversity and informative sites.
A web interface to analyze sequence divergence and diversity.
A web interface to detect informative sites in a set of aligned nucleotide or amino acid sequences.
A web database to store, retrieve and analyze HIV immunology data (ELISpot, HLA, etc.).
A web database to store, search and retrieve lab used HIV primers.
A web service to track scientific literatures via user-specified journals and keywords.
A web interface that estimates maximum likelihood phylogenetic tree from a set of aligned nucleotide or amino-acid sequences,
re-roots the tree at the least squares point (COT) and reconstructs the COT sequence.
A test for the detection of latent reservoirs.
A test for the detection of continued viral replication under antiviral therapies.
A tool to pull branch lengths from newick tree and returns divergence and diversity.
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
- UniSeq A tool to identify and extract unique sequences
- ChromatQuantitator A tool to quantitate mixed base composition in Sanger sequencing chromatograms
Perl scripts and libraries
For a complete list of services please visit the CFAR Molecular Profiling and Computational Biology core web page
These tools were developed in part with funding from the University of Washington Center for AIDS Research (CFAR), an NIH funded program under award number P30AI027757
which is supported by the following NIH Institutes and Centers (NIAID, NCI, NIMH, NIDA, NICHD, NHLBI, NIA).