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BASEML (in paml version 4.5, December 2011) Alignments/alignment.phylip F84 dGamma (ncatG=5)
Nonhomo: 3 fix_kappa 0
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: F84 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo -0.0000(-0.5000)
Gorilla_go -0.0000(-0.5000) -0.0000(-0.5000)
Pongo_pygm 0.0000(-0.5000) -0.0000(-0.5000) -0.0000(-0.5000)
Macaca_mul 0.0092( 0.4161) 0.0139( 1.3980) 0.0139( 1.4011) 0.0092( 0.4161)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 36): -320.002115 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.001476 0.000235 0.000004 0.000429 4.835353 4.835389 4.921462 71.977119 78.452939 4.967489 1.338428 0.115916 0.255762 0.286100 0.000000 0.106938 0.808417 0.000000 0.000000 0.988672 0.170030 0.288518 0.239140 0.000000 0.000639 0.986652 0.151289 0.666890 0.001952 0.202281 0.162318 0.369718 15.213973
tree length = 0.00216
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.001476): 0.000004, Gorilla_go: 0.000235): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.000429);
Detailed output identifying parameters
kappa under F84 (in order of branches): 4.83535 4.83539 4.92146 71.97712 78.45294 4.96749 1.33843
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.11592 0.25576 0.28610 0.34222 )
Node #2 ( 0.00000 0.10694 0.80842 0.08465 )
Node #3 ( 0.00000 0.00000 0.98867 0.01133 )
Node #4 ( 0.17003 0.28852 0.23914 0.30231 )
Node #5 ( 0.00000 0.00064 0.98665 0.01271 )
Node #6 ( 0.20228 0.16232 0.36972 0.26568 )
Node #7 ( 0.15129 0.66689 0.00195 0.17987 )
Node #8 ( 0.15129 0.66689 0.00195 0.17987 )
Note: node 6 is root.
alpha (gamma, K=5) = 15.21397
rate: 0.66961 0.85027 0.97864 1.11970 1.38178
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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