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TreeTransitionProb

TransitionProb[tree]
returns the invisible transtion probabiliy from tree.
TransitionProb[tree1, tree2]
returns the transtion probability between tree1 and tree2, based on the mSMC model, for the two trees of distance no greater than 2. If tree1=tree2, TransitionProb[tree1,tree2] = TransitionProb[tree1].
TreeTransitionProb[tree1, {e1, tc}]
returns the transtion probability between tree1 and tree2, where tree2 is produced from tree1 by the mSMC model, under the constraints that the recombination event occurs on branch e1 of tree1 and the emerging branch coaleces on a particular branch at time tc.
TreeTransitionProb[tree1, {e1, -1, e2}]
returns the transtion probability between tree1 and tree2, where tree2 is produced from tree1 by the mSMC model, under the constraints that the recombination event occurs on branch e1 of tree1 and the emerging branch coaleces with branch e2 of tree1.
  • A branch is given by a pair of nodes of the tree. Nodes of a tree is named by integers starting from 1.