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The capture gain probability p i capture(t) is p i capture t = { ∏ 1 ≤ k < i 1 - τ k t N k 1 - τ i t N i - 1 ( 1 - ∏ i < j ≤ M 1 - τ j t N j ) if 1 ≤ i < M 0 if i = M. (2).
Using the stochastic mapping results, genes with a gain probability of ≥0.8 were extracted on a branch-by-branch basis for functional categorization.
The observed numbers O m of multiple gains are computed by binning the total gain probabilities (including the ancestral branch gain probability), i.e. if the total Count reported gain probability for some family is between m − 0.5 and m + 0.5 for some integer m, O m is incremented.
Genes gains were assigned to the branch with the highest gain probability, provided that the presence probability at the ancestral node was ≤75% and ≥95% at the derived node.
The maximization of the approximate likelihood in Equation 3 with respect to S and α yields the estimate of the supergenome size S and the gain probability distribution in the supergenome characterized by α.
Protein sequences for all genes gained along terminal branches (i.e., recent acquisitions) with a gain probability of ≥0.8 were queried against the NCBI nonredundant database using BLASTp (E value ≤ 1 × 10−20).
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The power law above is the simplest non-trivial one-parameter distribution with a broad range of gain probabilities.
We also utilized the posterior gain probabilities computed by Count to estimate the size of the reservoir (supergenome) from which gains originate.
The total number of gains K is estimated as the sum of Count reported gain probabilities over all branches and families plus the sum of the probabilities of presence at the root node.
Figure 2 Fixed Gain outage probability.
To ensure asymptotic agility gain with probability one, a pairing protocol is developed.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com