
seed used = 1015636313

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: 13):  -2618.197687   +0.000000
   6..7     7..8     8..1     8..2     7..3     6..4     6..5  
  0.10250  0.02916  0.05643  0.07088  0.07313  0.27435  0.43314  0.88456  0.03076  0.00001  0.06841  0.01834  0.22539

tree length =   1.03958

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

(((Human: 0.056428, Chimpanzee: 0.070879): 0.029155, Gorilla: 0.073129): 0.102499, Orangutan: 0.274348, Gibbon: 0.433137);

Detailed output identifying parameters

Parameters  in the rate matrix (REV) (Yang 1994 J Mol Evol 39:105-111):

Rate parameters:    0.88456  0.03076  0.00001  0.06841  0.01834
Base frequencies:   0.25318  0.32894  0.31196  0.10592
Rate matrix Q, Average Ts/Tv =  10.5773
   -1.286667    1.245580    0.041083    0.000005
    0.958724   -1.058394    0.091353    0.008317
    0.033343    0.096326   -0.583102    0.453433
    0.000011    0.025828    1.335427   -1.361266

alpha (gamma, K=4) =  0.22539
rate:   0.00116  0.04959  0.44664  3.50262
freq:   0.25000  0.25000  0.25000  0.25000

check convergence..
