Five randomly chosen example segmentations on simulations from our simple bidirectional introgression scenario.

Each example shows the input alignments for the two populations (labeled “pop 1” and “pop 2” respectively), the true introgressed alleles for these two populations (labeled “pop 1 (y)” and “pop 2 (y)” respectively), the introgressed alleles inferred by IntroUNET (“pop 1 (pred)” and “pop 2 (pred)”), and IntroUNET’s inferred introgression probabilities (labelled “prob”, and scaled according to the color bar shown with the third example). Alignments and introgressed histories, true and predicted, are shown in the same format as in Fig 1.

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