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Flowchart of refinement process. (A) Overall process. (B) Subprocess for haplotype optimisation. (C) Subprocess for considering recombination, merging, and splitting; merging decreases the number of haplotypes by one, while splitting increases this number by one. Support for these three operations is evaluated by considering a penalised log likelihood equal to −0.5 times the Akaike Information Criterion.
