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Such computations are applied when computing term III of Equation 7, or when computing Equation 5. Term III of Equation 7 is computed once for every pair of subtrees T u v and S u ′ v ′, in O (min (d u, d u ′ ) 3 + d u d u ′ ) running time (Theorem 1, see also Section 'Reducing MCM to Min-Cost Max-Flow').
Thus, the complexity of computing Equation (4) for this partition is the following.
We could not dramatically simplify the full expression so we leave it in this form and note that it can be readily calculated (as above) by inserting Equations 47 50 into Equation 55 then computing Equation 73.
For h = 1 2, Equation 43 gives Figures 6 and 7 illustrate the variance of the admixture fraction under the special case of constant admixture, computing Equation 43 for different sets of values of the introgression parameters.
Although different functions ω may require different algorithms for computing the value Pr[ F| Y, X, k], we found that functions of the form ω(Ψ X ) = σ(|Ψ X |, l(Ψ X )) where l(Ψ X ) = ∑ X i, j ∈Ψ X | X i, j | denotes the sum of the lengths of the elements of Ψ X, admit particularly efficient algorithms for computing Equation (1).
Similar(55)
From the conditional matrix P, a symmetric overlap matrix O was also computed (Equation 4).
In Section 2.3, we explain how we compute Equation (1) efficiently for i > 0 (Step 2).
To compute Equation (10), we numerically approximate the integral using the rectangle method with the midpoint rule, computing each of the probabilities using the pruning algorithm.
In case a rooted alignment is sought, the algorithm can compute Equation 5 in line 3 only with respect to the two roots, and avoid the computation of Equation 6.
For a given value of the sample size g, we first compute Equation (4) for each of the 2 J − 1 non-empty combinations possible for a set of J populations.
Because and are invariant under any multiplication of γ and by an arbitrary constant, it is enough to determine the ratio between γ and in order to compute Equation (6).
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