
seed used = 1015640329

BASEML (in paml version 4, June 2007)  brown.nuc  REV dGamma (ncatG=4)
Frequencies..
                                    T      C      A      G
Human                          0.2570 0.3307 0.3050 0.1073
Chimpanzee                     0.2648 0.3240 0.3106 0.1006
Gorilla                        0.2581 0.3251 0.3117 0.1050
Orangutan                      0.2369 0.3453 0.3151 0.1028
Gibbon                         0.2492 0.3196 0.3173 0.1140

Homogeneity statistic: X2 = 0.00429 G = 0.00428 

Average                        0.253184 0.328939 0.311955 0.105922

# constant sites:    613 (68.49%)
ln Lmax (unconstrained) = -2476.965133

Distances: TN93 (kappa)  (alpha set at 0.50)
This matrix is not used in later m.l. analysis.

Human            
Chimpanzee         0.1214(42.4634)
Gorilla            0.1485(31.9110)  0.1562(28.5860)
Orangutan          0.2700(11.3980)  0.3101(13.1537)  0.2944(13.5463)
Gibbon             0.3217( 9.5815)  0.3573(10.5068)  0.3544(10.2059)  0.3501( 8.2174)

TREE #  1:  (((1, 2), 3), 4, 5);  MP score: 357.00
lnL(ntime:  7  np: 16):  -2616.073763   +0.000000
   6..7     7..8     8..1     8..2     7..3     6..4     6..5  
  0.13139  0.03549  0.05799  0.07461  0.07435  0.35015  0.54460  0.86726  0.02648  0.00001  0.04929  0.01110  0.23500  0.34587  0.32300  0.19249

tree length =   1.26858

(((Human, Chimpanzee), Gorilla), Orangutan, Gibbon);

(((Human: 0.057986, Chimpanzee: 0.074612): 0.035490, Gorilla: 0.074352): 0.131393, Orangutan: 0.350152, Gibbon: 0.544599);

Detailed output identifying parameters
kappa under REV:  0.86726  0.02648  0.00001  0.04929  0.01110
base frequency parameters
  0.23500  0.34587  0.32300  0.09613Rate parameters:    0.86726  0.02648  0.00001  0.04929  0.01110
Base frequencies:   0.23500  0.34587  0.32300  0.09613
Rate matrix Q, Average Ts/Tv =  12.8767
   -1.409681    1.370596    0.039081    0.000004
    0.931255   -1.008875    0.072745    0.004875
    0.028434    0.077896   -0.545575    0.439245
    0.000011    0.017541    1.475875   -1.493427

alpha (gamma, K=4) =  0.19249
rate:   0.00041  0.02956  0.36379  3.60625
freq:   0.25000  0.25000  0.25000  0.25000

