Table 2.

Perturbation analysis on local MSA probabilities in case (IV)

(∆L D1, ∆L D2)	0.01 indels/site	0.04 indels/site	0.1 indels/site	0.2 indels/site
(2, 1)	0.004	0.016	0.037	0.067
(3, 1)	0.016	0.063	0.150	0.279
(3, 2)	0.012	0.049	0.118	0.225
(10, 1)	0.050	0.190	0.432	0.751
(10, 2)	0.060	0.225	0.509	0.895
(10, 8)	0.060	0.231	0.543	0.980
(10, 9)	0.047	0.182	0.421	0.740
(30, 1)	0.140	0.487	0.915	1.203
(30, 5)	0.163	0.563	1.118	1.645
(30, 25)	0.173	0.620	1.251	1.850
(30, 29)	0.139	0.486	0.909	1.189
(100, 1)	0.418	0.985	1.180	1.304
(100, 99)	0.418	0.981	1.170	1.290

Each cell shows the ratio of the total next-parsimonious contribution to the total parsimonious contribution. In each local MSA, the first, second and third sequences have ∆L ^D1 sites, ∆L ^D2 (<∆L ^D1) sites and zero site, respectively, in between the PASs. Each column is labeled with the expected number of indels per site along each of the three branches. The ratios that are less than 0.5 are shown in boldface. This table is identical to Table 3 of [43]. See section M1 of Methods for the parameter setting