HIV fitness landscape

Infer the fitness landscape of HIV-1 from longitudinal, deep sequencing intrapatient data.

Results

• The mutation rates are in data/mutation_rates/mutation_rate_*.tsv in logarithms of 10, where the star covers the variation of parameters for the selection of the sites (see Fig. S2) and whether or not env was included. The actual file for Fig 1 is data/mutation_rates/mutation_rate_0.03_gp120.tsv.
• The approximately neutral sites that contribute to the mutation rates are in data/mutation_rates/mutation_rate_positions_*.txt, in 0-based HXB2 reference coordinates. The star has the same value like above. The actual file for Fig 1 is data/mutation_rates/mutation_rate_positions_0.03_gp120.txt.
• The site-specific fitness costs in HXB2 coordinates are located in data/nuc_*_selection_coefficients_any.tsv, where * indicates any of several genomic regions: gag, pol, env, nef, vif, vpu, and vpr.

Folders

• src: scripts
• data: additional data (HIVEVO_access data must be present too)