Fig 1. TRAILS is a HMM that reconstructs the time-resolved multi-species ARG for three genomes.
TRAILS extends the isolation model (B) [19] to three species, by combining the time discretization of PSMC-like models (A) [8] with the topologically aware hidden states of CoalHMM (C) [20, 21]. The resulting hidden states of TRAILS (D) are three-leaved genealogies with two discretized coalescent events and one of four possible topologies. A full list of the 27 possible hidden states when nAB = nABC = 3 can be consulted in Fig K in S1 Text.