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seed used = 1
BASEML (in paml version 4.3, August 2009) Alignments/alignment.phylip F84 dGamma (ncatG=5)
Nonhomo: 4 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 0.200901 0.163063 0.370270 0.265766
# 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: 39): -320.146887 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.000485 0.000498 0.000004 0.000348 5.000016 4.999600 5.000097 9.743061 10.117731 5.000039 1.314201 0.261069 0.251981 0.247918 0.000007 0.578725 0.420347 0.585363 0.000004 0.413990 0.250161 0.248718 0.270955 0.000000 0.019350 0.978596 0.202699 0.162156 0.369406 0.244028 0.259610 0.255234 0.250790 0.276525 0.253662 3.614229
tree length = 0.00135
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.000485): 0.000004, Gorilla_go: 0.000498): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.000348);
Detailed output identifying parameters
kappa under F84 (in order of branches): 5.00002 4.99960 5.00010 9.74306 10.11773 5.00004 1.31420
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.26107 0.25198 0.24792 0.23903 )
Node #2 ( 0.00001 0.57873 0.42035 0.00092 )
Node #3 ( 0.58536 0.00000 0.41399 0.00064 )
Node #4 ( 0.25016 0.24872 0.27096 0.23017 )
Node #5 ( 0.00000 0.01935 0.97860 0.00205 )
Node #6 ( 0.20270 0.16216 0.36941 0.26574 )
Node #7 ( 0.24403 0.25961 0.25523 0.24113 )
Node #8 ( 0.25079 0.27652 0.25366 0.21902 )
Note: node 6 is root.
alpha (gamma, K=5) = 3.61423
rate: 0.39382 0.67251 0.91138 1.20323 1.81907
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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