V-Profiler takes a read alignment and a list of accepted variants at each location in the alignment (such as would be generated by V-Phaser) and analyzes the intra-host diversity of a genome. This can be done at the nucleotide level over the whole sequence, at the codon level for each gene specified in a list, and at the haplotype level for any region delimited (note that the region must not exceed a read length, and is preferably of shorter length such as an epitope or a loop of interest). It will also output Heatmaps of the diversity at the codon level using R.
V-Profiler is available as part of the V-Phaser software package
Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Steeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Gunthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereya F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM(2012) Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. PLoS Pathogens 8(3): e1002529.
Support for this tool was provided by the National Institute of Allergy and Infectious Diseases through the Microbial Sequencing Center and Genome Sequencing Center for Infectious Diseases, by grants made by the Bill & Melinda Gates Foundation (awarded to the Ragon Institute), the NIAID-DAIDS (awarded to Ragon Institute), and through internal support at the Broad Institute.