HIV Sequence Database
|
Programs and Tools
Search Interface retrieves HIV and SIV sequences, which can then be aligned and used to build trees Geography Search Interface retrieves HIV sequences based on geographical distribution Tools for working with sequences a complete list of our online tools, organized by function Alignments
HIV Premade Alignments includes Consensus and Ancestral Sequences, Subtype Reference Alignments (for use in trees, subtyping, and recombination analysis), and Complete Alignments (based on all sequences in the database) |
Information
HIV Sequence Compendia print or order a copy of our annual compendium and review articles Tutorials and other information unpublished web-based content posted on this site Links to other HIV/AIDS tools and information About this website
FAQ questions and answers that give general information about this website How to Cite this Database explains how to refer to this database in publications |
HIV Molecular Immunology 2008 is now available on-line. The PDF version is hypertext enabled and features `clickable' table-of-contents, indexes, references and links to external web sites. 13 August 2008
Updates for the 2008 Molecular Immunology Database now available on-line. Updated epitope maps and epitope summary tables are also on-line. 31 July 2008
The 2007 HIV-1, HIV-2/SIVsmm and PIV alignments are now available. The same webpage also has a new set of reference alignments. 09 July 2008
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
