Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Resources

Multi-Drug Resistant Panels
Panels of prototypical infectious multidrug resistant HIV-1 clones. The panels include clones with each of the published drug resistance mutations in the combinations that occur most frequently in HIV-infected individuals.

Multi-Drug Resistant Panels

Programs
Syn-SCAN calculates the synonymous and nonsynonmous mutation rates between sequences containing ambiguous nucleotides
Syn-SCAN Page

PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment.
Download pyromap.tar.gz

G-to-A hypermutation filter generation using expectation maximization. Given a table of aggregated values and a set of preliminary filter constants, this program will construct a set of frequency distributions characterizing the hypermutated and non-hypermutated sequence subsets. The filter constants can then be exported as a perl library, python file, or in human-readable statements. Manuscript submitted
Download g2a_filter_em.tar.bz2