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seed used = 1024367525
BASEML (in paml version 4.4c, August 2010) Alignments/alignment.phylip F81 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 0.2009 0.1631 0.3703 0.2658
# constant sites: 218 (98.20%)
ln Lmax (unconstrained) = -316.049385
Distances: F81 (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): -326.318169 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004517 0.004521 0.000004 0.009071 999.000000
tree length = 0.01813
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004517): 0.000004, Gorilla_go: 0.004521): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009071);
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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