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BASEML (in paml version 4.6, August 2012) Alignments/alignment.phylip JC69 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
Printing out site pattern counts
5 4 P
Homo_sapie TTTT
Pan_troglo TTCT
Gorilla_go TCTT
Pongo_pygm TTTT
Macaca_mul TTTC
218 1 1 2
Distances: JC69 (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo 0.0045
Gorilla_go 0.0045 0.0092
Pongo_pygm 0.0000 0.0045 0.0045
Macaca_mul 0.0092 0.0139 0.0139 0.0092
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 8): -336.366238 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004514 0.004516 0.000004 0.009061 999.000000
tree length = 0.01811
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004514): 0.000004, Gorilla_go: 0.004516): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009061);
Detailed output identifying parameters
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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