General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation

Table 3 Comparison of Kim-Sinha’s probability with ab initio probability for case (iv) local PWA

Each row gives values for a local PWA with ∆L ^A ancestral sites and ∆L ^D descendant sites in between a pair of PASs. See section M1 of Methods for the parameter setting. When λ _I = λ _D, the ratio for (ΔL ^A, ΔL ^D) = (L ₁, L ₂) is identical to that for (ΔL ^A, ΔL ^D) = (L ₂, L ₁). Thus, we only showed the results for ΔL ^A ≥ ΔL ^D. The ratios less than 2 are in boldface. This table is a modified version of Table 4 of [43]
^a The ratio of the ab initio probability to the corresponding probability given by the HMM of Kim and Sinha [36], in the limit where the time interval (or branch length) approaches zero
^b The portion of the ratio contributed by overlapping indels (such as those in panels d and e of Additional file 1: Figure S3)

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