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BASEML (in paml version 4.7, January 2013) Alignments/alignment.phylip UNREST 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: 19): -319.763591 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004516 0.004506 0.000004 0.009160 816.874140 256.544253 0.000010 998.654170 0.000010 0.000010 137.750265 0.000010 0.715255 0.000010 0.000010 203.876618
tree length = 0.01820
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.00000, Pan_troglo: 0.00452): 0.00000, Gorilla_go: 0.00451): 0.00000, Pongo_pygm: 0.00000, Macaca_mul: 0.00916);
Detailed output identifying parameters
Parameters in the rate matrix (UNREST) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 816.87414 256.54425 0.00001 998.65417 0.00001 0.00001 137.75026 0.00001 0.71525 0.00001 0.00001
Base frequencies: 0.19950 0.16319 0.37155 0.26575
rate matrix Q, Average Ts/Tv (similar to kappa/2) = 3.1893
-2.503110 1.904873 0.598237 0.000000
2.328767 -2.328767 0.000000 0.000000
0.321221 0.000000 -0.322889 0.001668
0.000000 0.000000 0.002332 -0.002332
alpha (gamma, K=5) = 203.87662
rate: 0.90395 0.96166 0.99840 1.03609 1.09990
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
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