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BASEML (in paml version 4.5, December 2011) Alignments/alignment.phylip UNREST 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: 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: 19): -319.761370 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004637 0.004632 0.000004 0.009230 828.247975 274.138529 0.000010 999.000000 0.000010 0.000010 146.357862 0.000010 0.715129 0.000031 0.000010 336.641419
tree length = 0.01852
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004637): 0.000004, Gorilla_go: 0.004632): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009230);
Detailed output identifying parameters
Parameters in the rate matrix (UNREST) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 828.24798 274.13853 0.00001 999.00000 0.00001 0.00001 146.35786 0.00001 0.71513 0.00003 0.00001
Base frequencies: 0.19835 0.16445 0.37152 0.26568
rate matrix Q, Average Ts/Tv (similar to kappa/2) = 3.0262
-2.517739 1.891634 0.626104 0.000000
2.281614 -2.281614 0.000000 0.000000
0.334266 0.000000 -0.335900 0.001633
0.000000 0.000000 0.002284 -0.002284
alpha (gamma, K=5) = 336.64142
rate: 0.92490 0.97034 0.99903 1.02829 1.07743
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
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