HIV Molecular Immunology Database

We have a new web tool, Heatmap. Heatmap is a web interface for analysis of quantitative data that may be particularly helpful for interpretations of immunological data, providing heat maps and hierarchical clustering. 26 June 2008

The Codon alignment tool can restore codons in your alignment so that the resulting alignment can be immediately translated. Currently this tool requires an input reading frame (or does its work for all 3 frames). In the future we will connect it to the reference sequence and the 'locate' tool so that it can find the correct reading frame automatically. 21 June 2008

Try out Phyloplace! This tool was designed to help users decide whether their sequence fits inside a currently known genotype subtype, or would be better classified as a new one. It can use either an intuitive distance-based method or the phylogenetic tree-based Branching index, and produces user-friendly graphical output for both. The tool also shows some promise for easily finding potential recombinants. 20 June 2008

We added a beta version of the new tool HIValign, which uses our HIV HMM alignment model to align user sequences. It can also codon-align the sequences, and separate individual HIV genes, and thus is a near-successor to Gene cutter. Please note that the tool has not yet been extensively tested. We would appreciate bug reports and other feedback. 19 June 2008

HIV Sequence Compendium 2008 is now available on-line. The printed copy is at the printers and should begin shipping in a few weeks. 05 June 2008