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HIV sequence database

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

Genome Browser uses jBrowse to display diverse data about the HIV-1 genome and proteome

Tools for working with sequences lists all our online tools, organized by function


HIV Premade Alignments includes Consensus and Ancestral Sequences, Subtype Reference Alignments, and Complete Alignments


HIV Sequence Compendium print or order our annual publication

Tutorials and other information unpublished web-based content

Links to other HIV/AIDS tools and information

About this website

FAQ general information about this website

Site Statistics usage information for

How to Cite this Database

Editorial Board


An HIV Database workshop presented by Los Alamos National Laboratory staff will be included as part of the IEDB User Workshop in October 2016 in San Diego, CA. For information and registration, see

Archived News News

New vaccine design tool: Epigraph
The Epigraph tool generates Epigraph sequences based on an input population of diverse sequences. Like Mosaic proteins, Epigraphs are artificial proteins that combine to maximize the potential epitope coverage (PTE) of a diverse population of protein sequences. Epigraph sequences can be used for either vaccine or reagent design. The basic input for the program is a diverse set of sequences that is representative of a viral population of interest. The output is a user specified number of artificial but intact sequences that, for a given number of sequences, will provide optimal epitope coverage. 01 September 2016

Immune Epitope Database User Workshop October 24 - 25, 2016
The Immune Epitope Database (IEDB) is an NIH-supported, freely available resource that provides access to published data related to antibody and T-cell epitopes, as well as online tools for prediction and analysis. An HIV Database workshop presented by Los Alamos National Laboratory staff will be included as part of the IEDB User Workshop in October 2016 in San Diego, California. For more information and registration, contact the IEDB at 31 August 2016

HIV Sequence Compendium 2016
HIV Sequence Compendium 2016 is now available online. The 2016 Compendium is only available online in PDF format. 11 August 2016

Improvements to Pixel
The Pixel tool provides quality control for alignments by producing a graphic image with colored pixels corresponding to nucleotide or amino acid residues. A new Advanced version of the tool provides new color schemes and allows users more control over the appearance of the image. 07 July 2016

Improvements to Highlighter
The Highlighter tool provides a graphical view of sequence matches, mismatches, transitions, transversions, silent, and non-silent mutations in protein or nucleotide alignments. The major new feature is the highlighting of glycosylation motifs in amino acid alignments. Minor improvements include the ability to change the width of the tic marks, revised logic for transition/transversion highlighting, and new options for matches highlighting. 06 July 2016

last modified: Mon Sep 12 13:17 2016

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