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BASEML (in paml version 4.6, August 2012) Alignments/alignment.phylip T92 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: T92 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0046(999.0000)
Gorilla_go 0.0046(999.0000) 0.0093(999.0000)
Pongo_pygm 0.0000(999.0000) 0.0046(999.0000) 0.0046(999.0000)
Macaca_mul 0.0092( 2.0615) 0.0139( 4.1830) 0.0139( 4.1940) 0.0092( 2.0615)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 9): -332.579040 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004516 0.004520 0.000004 0.009084 6.155630 999.000000
tree length = 0.01814
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004516): 0.000004, Gorilla_go: 0.004520): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009084);
Detailed output identifying parameters
Parameters (kappa) in the rate matrix (T92) (Yang 1994 J Mol Evol 39:105-111):
6.15563
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
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