Figure 9.

Estimated absorption times in diCal using the leave-one-out SMCSD method vs. the true coalescence times for a 100-kb region. The data were simulated using ms for n = 6 haplotypes, assuming a constant population size. The true coalescence time at each site, obtained from ms, was taken as the time the ancestral lineage of a left-out haplotype joined the rest of the coalescent tree at that site. Shown is the true coalescence time for the nth haplotype and our corresponding inferred absorption times, obtained from the posterior decoding and the posterior mean. Our estimates generally track the true coalescence times closely.