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
|
BASEML (in paml version 4.7, January 2013) Alignments/alignment.phylip F81 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: F81 (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0045
Gorilla_go 0.0045 0.0092
Pongo_pygm 0.0000 0.0045 0.0045
Macaca_mul 0.0092 0.0139 0.0139 0.0092
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 11): -326.289558 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004524 0.004524 0.000004 0.009076 0.203159 0.167697 0.368137 999.000000
tree length = 0.01814
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.00000, Pan_troglo: 0.00452): 0.00000, Gorilla_go: 0.00452): 0.00000, Pongo_pygm: 0.00000, Macaca_mul: 0.00908);
Detailed output identifying parameters
Base frequencies:
0.20316 0.16770 0.36814 0.26101
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
|
