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seed used = 1
BASEML (in paml version 4.3, August 2009) 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): -319.774033 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004533 0.004529 0.000004 0.009175 999.000000 159.951743 0.000010 0.000010 0.000010 199.304547
tree length = 0.01825
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004533): 0.000004, Gorilla_go: 0.004529): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009175);
Detailed output identifying parameters
Parameters in the rate matrix (REV) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 999.00000 159.95174 0.00001 0.00001 0.00001
Base frequencies: 0.20090 0.16306 0.37027 0.26577
Rate matrix Q, Average Ts/Tv = 2.7588
-2.483313 1.821186 0.662127 0.000000
2.243782 -2.243782 0.000000 0.000000
0.359256 0.000000 -0.362227 0.002971
0.000000 0.000000 0.004140 -0.004140
alpha (gamma, K=5) = 199.30455
rate: 0.90287 0.96121 0.99836 1.03649 1.10106
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
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