1
2seed used = 1024367525
3
4BASEML (in paml version 4.4c, August 2010)  Alignments/alignment.phylip  K80 dGamma (ncatG=5)
5Frequencies..
6                                    T      C      A      G
7Homo_sapie                     0.2027 0.1622 0.3694 0.2658
8Pan_troglo                     0.1982 0.1667 0.3694 0.2658
9Gorilla_go                     0.2072 0.1577 0.3694 0.2658
10Pongo_pygm                     0.2027 0.1622 0.3694 0.2658
11Macaca_mul                     0.1937 0.1667 0.3739 0.2658
12
13Homogeneity statistic: X2 = 0.00092 G = 0.00092
14
15Average                         0.2009  0.1631  0.3703  0.2658
16
17# constant sites:    218 (98.20%)
18ln Lmax (unconstrained) = -316.049385
19
20Distances:  K80 (kappa)  (alpha set at 0.50)
21This matrix is not used in later m.l. analysis.
22
23Homo_sapie
24Pan_troglo         0.0046(999.0000)
25Gorilla_go         0.0046(999.0000)  0.0093(999.0000)
26Pongo_pygm         0.0000(999.0000)  0.0046(999.0000)  0.0046(999.0000)
27Macaca_mul         0.0092( 2.0206)  0.0139( 4.1043)  0.0139( 4.1043)  0.0092( 2.0206)
28
29TREE #  1:  (((1, 2), 3), 4, 5);  MP score: 4.00
30lnL(ntime:  7  np:  9):   -334.912612    +0.000000
31   6..7     7..8     8..1     8..2     7..3     6..4     6..5
32 0.000004 0.000004 0.000004 0.004516 0.004518 0.000004 0.009091 6.038381 999.000000
33
34tree length =   0.01814
35
36(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
37
38(((Homo_sapie: 0.000004, Pan_troglo: 0.004516): 0.000004, Gorilla_go: 0.004518): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009091);
39
40Detailed output identifying parameters
41
42Parameters (kappa) in the rate matrix (K80) (Yang 1994 J Mol Evol 39:105-111):
43  6.03838
44
45alpha (gamma, K=5) = 999.00000
46rate:   0.95611  0.98294  0.99967  1.01660  1.04468
47freq:   0.20000  0.20000  0.20000  0.20000  0.20000
48
49check convergence..
50