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seed used = 1
BASEML (in paml version 4.3, August 2009) Alignments/alignment.phylip HKY85 dGamma (ncatG=5)
Frequencies..
T C A G
Homo_sapie 0.2027 0.1622 0.3694 0.2658
Pan_troglo 0.1982 0.1667 0.3694 0.2658
Gorilla_go 0.2072 0.1577 0.3694 0.2658
Pongo_pygm 0.2027 0.1622 0.3694 0.2658
Macaca_mul 0.1937 0.1667 0.3739 0.2658
Homogeneity statistic: X2 = 0.00092 G = 0.00092
Average 0.200901 0.163063 0.370270 0.265766
# constant sites: 218 (98.20%)
ln Lmax (unconstrained) = -316.049385
Distances:HKY85 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0093(999.0000)
Gorilla_go 0.0093(999.0000) 0.0194(999.0000)
Pongo_pygm 0.0000(999.0000) 0.0093(999.0000) 0.0093(999.0000)
Macaca_mul 0.0142( 3.6925) 0.0245( 7.6730) 0.0246( 7.7118) 0.0142( 3.6925)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 9): -325.068648 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004519 0.004520 0.000004 0.009085 5.317786 999.000000
tree length = 0.01814
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004519): 0.000004, Gorilla_go: 0.004520): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009085);
Detailed output identifying parameters
Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
5.31779
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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