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seed used = 1105670833
BASEML (in paml version 4.1, August 2008) Alignments/alignment.phylip REV 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: TN93 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0047(999.0000)
Gorilla_go 0.0047(999.0000) 0.0097(999.0000)
Pongo_pygm 0.0000(999.0000) 0.0047(999.0000) 0.0047(999.0000)
Macaca_mul 0.0093( 3.6925) 0.0145( 7.6730) 0.0145( 7.7118) 0.0093( 3.6925)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 13): -319.768811 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.00000 0.00000 0.00000 0.00454 0.00454 0.00000 0.00918 999.00000 145.58264 0.00001 0.00001 0.00001 267.04366
tree length = 0.01826
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004540): 0.000000, Gorilla_go: 0.004536): 0.000000, Pongo_pygm: 0.000004, Macaca_mul: 0.009176);
Detailed output identifying parameters
Parameters in the rate matrix (REV) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 999.00000 145.58264 0.00001 0.00001 0.00001
Base frequencies: 0.20090 0.16306 0.37027 0.26577
Rate matrix Q, Average Ts/Tv = 3.0311
-2.483179 1.865778 0.617401 0.000000
2.298721 -2.298721 0.000000 0.000000
0.334989 0.000000 -0.338033 0.003044
0.000000 0.000000 0.004241 -0.004241
alpha (gamma, K=5) = 267.04366
rate: 0.91585 0.96661 0.99878 1.03167 1.08709
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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