A panel of 12 prototypical infectious multidrug resistant HIV-1 reverse transcriptase (RT) clones. The panel includes clones with each of the published nucleoside analog RT inhibitor (NRTI) mutations in the combinations that occur most frequently in HIV-infected individuals.
Syn-SCAN calculates the synonymous and nonsynonmous mutation rates between sequences containing ambiguous nucleotides
PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment.
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