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seed used = 1024367521
BASEML (in paml version 4.4, January 2010) 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): -319.779425 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.004517 0.004512 0.000004 0.009150 176.027758 58.196436 0.000010 212.341161 0.000010 0.000010 31.047280 0.000010 0.714948 0.000010 0.000010 65.711557
tree length = 0.01820
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.004517): 0.000004, Gorilla_go: 0.004512): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009150);
Detailed output identifying parameters
Parameters in the rate matrix (UNREST) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 176.02776 58.19644 0.00001 212.34116 0.00001 0.00001 31.04728 0.00001 0.71495 0.00001 0.00001
Base frequencies: 0.19827 0.16437 0.37165 0.26571
rate matrix Q, Average Ts/Tv (similar to kappa/2) = 3.0477
-2.507430 1.884422 0.623008 0.000000
2.273166 -2.273167 0.000000 0.000000
0.332369 0.000000 -0.340023 0.007654
0.000000 0.000000 0.010705 -0.010705
alpha (gamma, K=5) = 65.71156
rate: 0.83360 0.93108 0.99504 1.06194 1.17834
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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