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BASEML (in paml version 4.7, January 2013) Alignments/alignment.phylip TN93 dGamma (ncatG=5)
nparK: 1 K: 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): -320.889683 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004535 0.004544 0.000004 0.009206 21.547157 0.000010 0.999527 0.998848 0.999064 1.001629
tree length = 0.01830
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.00000, Pan_troglo: 0.00454): 0.00000, Gorilla_go: 0.00454): 0.00000, Pongo_pygm: 0.00000, Macaca_mul: 0.00921);
Detailed output identifying parameters
Parameters (kappa) in the rate matrix (TN93) (Yang 1994 J Mol Evol 39:105-111):
21.54716 0.00001
rate: 0.99953 0.99885 0.99906 1.00163 1.00093
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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