Fig. 3.

RATS-LD can estimate recombination rates in conditions that mimic HIV intrahost evolution. A) Recombination rate estimates from simulations performed with HIV-like selective conditions recapture known ρ values. B) Recombination rate estimates from simulated subdivided populations interconnected by bidirectional migration. Each generation, a proportion m of each subpopulation emigrates from the other subpopulation ($m={10}^{-2},{10}^{-3},{10}^{-4},{10}^{-5}$). C) Recombination rate estimates in datasets simulated under a range of effective population sizes ($N_e=5\times {10}^3$ to $5\times {10}^5$). We plot ten estimation groups for $N_e$ values $<{10}^5$ and five estimation groups for $N_e$ values $\ge {10}^5$. In all three panels, each point represents the median estimate over 1,000 bootstraps. For full details on all of the specific simulation scenarios, see Materials and methods.