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RandomSequentialTrees

RandomSequentialTrees[tree, , x0, x1]
generates local trees along chromsomes based on the modified Sequential Markov Coalescent process with recombation rate , starting from tree at x=x0 and continuing until x=x1. Returns a list with each element consisting of change-point location, transition operator from the tree before recombation event, and local tree on and after change-point.
  • There are two settings for x0 and x1. First, the sequences are represented continuously from 0 to 1 and thus 0≤x0<x1≤1. Second, the sequences are represented discretely in unit of bp, and thus both x0 and x1 are positive integers and x0<x1.