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
49
50
51
52
53
54
|
BASEML (in paml version 4.6, August 2012) Alignments/alignment.phylip UNREST dGamma (ncatG=5)
Frequencies..
T C A G
Homo_sapie 0.20270 0.16216 0.36937 0.26577
Pan_troglo 0.19820 0.16667 0.36937 0.26577
Gorilla_go 0.20721 0.15766 0.36937 0.26577
Pongo_pygm 0.20270 0.16216 0.36937 0.26577
Macaca_mul 0.19369 0.16667 0.37387 0.26577
Homogeneity statistic: X2 = 0.00092 G = 0.00092
Average 0.20090 0.16306 0.37027 0.26577
# constant sites: 218 (98.20%)
ln Lmax (unconstrained) = -316.049385
Distances: TN93 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0047(999.0000)
Gorilla_go 0.0047(999.0000) 0.0097(999.0000)
Pongo_pygm 0.0000(999.0000) 0.0047(999.0000) 0.0047(999.0000)
Macaca_mul 0.0093( 3.6925) 0.0145( 7.6730) 0.0145( 7.7118) 0.0093( 3.6925)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 19): -319.787136 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004500 0.004493 0.000004 0.009111 177.269147 53.250696 0.000482 213.581963 0.000010 0.008354 28.034463 0.000010 0.706440 0.000010 0.000010 46.095554
tree length = 0.01812
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004500): 0.000004, Gorilla_go: 0.004493): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009111);
Detailed output identifying parameters
Parameters in the rate matrix (UNREST) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 177.26915 53.25070 0.00048 213.58196 0.00001 0.00835 28.03446 0.00001 0.70644 0.00001 0.00001
Base frequencies: 0.19688 0.16340 0.37403 0.26568
rate matrix Q, Average Ts/Tv (similar to kappa/2) = 3.3537
-2.524784 1.941548 0.583231 0.000005
2.339266 -2.339357 0.000000 0.000091
0.307049 0.000000 -0.314786 0.007737
0.000000 0.000000 0.010953 -0.010953
alpha (gamma, K=5) = 46.09555
rate: 0.80286 0.91700 0.99293 1.07306 1.21415
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
|
