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Inference of Ancestral Recombination Graphs through Topological Data Analysis

Fig 5

Persistent homology of a sample of genetic sequences.

Barcode and Vietoris-Rips complexes at several values of the parameter ϵ, for the sample of sequences . Only the first homology group (H₁) is shown. At small ϵ the four sampled points are disconnected. Increasing ϵ leads to a loop, that appears as a single element of H₁. Further increasing ϵ fills in the loop, leading to a single connected surface. An ultra-minimal ARG explaining , and the corresponding tARG are shown in Fig 2 (bottom). The barcode only captures one of the R_min = 2 recombination events.

doi: https://doi.org/10.1371/journal.pcbi.1005071.g005