1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
seed used = 1024367525
BASEML (in paml version 4.4c, August 2010) Alignments/alignment.phylip T92 dGamma (ncatG=5)
Frequencies..
T C A G
Homo_sapie 0.2027 0.1622 0.3694 0.2658
Pan_troglo 0.1982 0.1667 0.3694 0.2658
Gorilla_go 0.2072 0.1577 0.3694 0.2658
Pongo_pygm 0.2027 0.1622 0.3694 0.2658
Macaca_mul 0.1937 0.1667 0.3739 0.2658
Homogeneity statistic: X2 = 0.00092 G = 0.00092
Average 0.2009 0.1631 0.3703 0.2658
# constant sites: 218 (98.20%)
ln Lmax (unconstrained) = -316.049385
Distances: T92 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0046(999.0000)
Gorilla_go 0.0046(999.0000) 0.0093(999.0000)
Pongo_pygm 0.0000(999.0000) 0.0046(999.0000) 0.0046(999.0000)
Macaca_mul 0.0092( 2.0615) 0.0139( 4.1830) 0.0139( 4.1940) 0.0092( 2.0615)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 9): -332.579040 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004516 0.004520 0.000004 0.009083 6.158672 999.000000
tree length = 0.01814
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004516): 0.000004, Gorilla_go: 0.004520): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009083);
Detailed output identifying parameters
Parameters (kappa) in the rate matrix (T92) (Yang 1994 J Mol Evol 39:105-111):
6.15867
alpha (gamma, K=5) = 999.00000
rate: 0.95611 0.98294 0.99967 1.01660 1.04468
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
|
