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BASEML (in paml version 4.7, January 2013) Alignments/alignment.phylip REV 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: 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): -319.774741 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004532 0.004530 0.000004 0.009182 998.999977 130.949079 0.000010 0.000010 0.000010 200.957527
tree length = 0.01826
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.00000, Pan_troglo: 0.00453): 0.00000, Gorilla_go: 0.00453): 0.00000, Pongo_pygm: 0.00000, Macaca_mul: 0.00918);
Detailed output identifying parameters
Parameters in the rate matrix (REV) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 998.99998 130.94908 0.00001 0.00001 0.00001
Base frequencies: 0.20090 0.16306 0.37027 0.26577
Rate matrix Q, Average Ts/Tv = 3.3698
-2.483036 1.913492 0.569543 0.000000
2.357507 -2.357507 0.000000 0.000000
0.309022 0.000000 -0.312144 0.003122
0.000000 0.000000 0.004349 -0.004349
alpha (gamma, K=5) = 200.95753
rate: 0.90327 0.96137 0.99838 1.03635 1.10064
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
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