BMC Genomics

Table 2 Shimodaira-Hasegawa test for incongruence

From: Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses

E1 as reference tree
Tree	deltaL	bp-RELL	p-KH	p-SH	p-WKH	p-WSH	c-ELW	p-AU
E1	0	1	1	1	1	1	1	0.999
E2	182.16	0	0	0.008	0	0	7.3e-33	0.000747
E4	639.14	0	0	0	0	0	3.8e-203	0.000845
E7	1048.70	0	0	0	0	0	0	1.8e-58
L1	381.21	0	0	0	0	0	3.8e-104	4.2e-05
L2	219.47	0	0	0.002	0	0	1.2e-40	2.4e-09
E2 as reference tree
Tree	deltaL	bp-RELL	p-KH	p-SH	p-WKH	p-WSH	c-ELW	p-AU
E1	137.43	0	0	0.023	0	0	1.3e-27	8.3e-05
E2	0	1	1	1	1	1	1	1
E4	288.35	0	0	0	0	0	1.3e-75	2.8e-07
E7	904.92	0	0	0	0	0	3.4e-299	6.7e-97
L1	273.21	0	0	0	0	0	5.9e-70	5.7e-44
L2	224.96	0	0	0	0	0	1.8e-60	5.1e-07
E4 as reference tree
Tree	deltaL	bp-RELL	p-KH	p-SH	p-WKH	p-WSH	c-ELW	p-AU
E1	79.74	0	0	0.012	0	0.004	0.000433	0.0217
E2	64.99	0.02	0.003	0.02	0.003	0.016	0.00211	0.104
E4	0	0.998	0.997	1	0.997	1	0.997	0.992
E7	311.86	0	0	0	0	0	8.7e-85	5.8e-114
L1	130.15	0	0	0	0	0	1.2e-23	6.4e-35
L2	84.83	0	0	0.004	0	0	1.1e-10	0.00483
E7 as reference tree
Tree	deltaL	bp-RELL	p-KH	p-SH	p-WKH	p-WSH	c-ELW	p-AU
E1	59,374	0.004	0.016	0.017	0.016	0.064	0.00429	0.0117
E2	71.02	0.001	0.007	0.007	0.007	0.031	0.000919	0.00182
E4	138.43	0	0	0	0	0	1.78e-20	0.014
E7	0	0.946	0.952	1	0.952	0.991	0.944	0.945
L1	39.42	0.0041	0.048	0.119	0.048	0.189	0.043	0.118
L2	59.86	0.008	0.022	0.025	0.022	0.063	0.00759	0.0321
L1 as reference tree
Tree	deltaL	bp-RELL	p-KH	p-SH	p-WKH	p-WSH	c-ELW	p-AU
E1	188.69	0	0	0	0	0	1.3e-25	7.6e-05
E2	218.51	0	0	0	0	0	4.1e-40	6.6e-48
E4	473.21	0	0	0	0	0	1.6e-133	0.000267
E7	899.66	0	0	0	0	0	3.5e-301	5.98e-65
L1	0	1	1	1	1	1	1	1
L2	149.83	0	0	0.005	0	0	9.9e-301	1.23e-10
L2 as reference tree
Tree	deltaL	bp-RELL	p-KH	p-SH	p-WKH	p-WSH	c-ELW	p-AU
E1	226.34	0	0	0	0	0	2.4e-51	1.3e-52
E2	220.29	0	0	0	0	0	1.8e-50	8.4e-12
E4	478.78	0	0	0	0	0	1.5e-149	4.2e-06
E7	1087.1	0	0	0	0	0	0	0.00124
L1	229.72	0	0	0	0	0	1.3e-42	2.01e-13
L2	0	1	1	1	1	1	1	1

deltaL: logL difference from the maximal logl in the set
bp-RELL: bootstrap proportion using RELL method [38]
p-KH: p-value of one sided [29]
p-SH: p-value of Shimodaira-Hasegawa test [22]
p-WKH: p-value of weighted KH test
p-WSH: p-value of weighted SH test
c-ELW: Expected Likelihood Weight [39]
p-AU: p-value of approximately unbiased (AU) test [30]

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