Center for AIDS Research

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 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

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.

A tool to reformat diagonal distance matrices into columnar output.

A tool to identify and extract unique sequences.

Command-line analysis of sequence divergence and diversity.

Automatically annotate sequences for bulk submission to GenBenk.

Reformat output from NetNLGlyc.

Reformat output from NetOLGlyc.

Relabel nodes in a Newick tree.

Calculate amino acid frequency for each position in an alignment.

Remove identical and overlapping sequences from an alignment.

Reformat output from LANL's sequence locator.

Format conversion between alignment formats, fasta sequence cleaner.

Report external branch lengths of a Newick tree.

Reformat column distance matrix into the input format of diverstest web tool.