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seed used = 1105670833
BASEML (in paml version 4.1, August 2008) 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): -319.978129 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.00000 0.00000 0.00000 0.00060 0.00130 0.00000 0.00009 4.99979 5.00001 5.00206 151.74249 155.82513 5.00348 1.37315 0.35979 0.10084 0.35087 0.00000 0.00015 0.96772 0.00001 0.00000 0.93271 0.25602 0.17843 0.35647 0.00000 0.00272 0.99564 0.20289 0.16225 0.36935 0.24928 0.26248 0.25794 0.24832 0.26850 0.25290 32.22404
tree length = 0.00200
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.000596): 0.000000, Gorilla_go: 0.001303): 0.000000, Pongo_pygm: 0.000004, Macaca_mul: 0.000094);
Detailed output identifying parameters
kappa under F84 (in order of branches): 4.99979 5.00001 5.00206 151.74249 155.82513 5.00348 1.37315
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.35979 0.10084 0.35087 0.18850 )
Node #2 ( 0.00000 0.00015 0.96772 0.03213 )
Node #3 ( 0.00001 0.00000 0.93271 0.06727 )
Node #4 ( 0.25602 0.17843 0.35647 0.20907 )
Node #5 ( 0.00000 0.00272 0.99564 0.00164 )
Node #6 ( 0.20289 0.16225 0.36935 0.26551 )
Node #7 ( 0.24928 0.26248 0.25794 0.23030 )
Node #8 ( 0.24832 0.26850 0.25290 0.23029 )
Note: node 6 is root.
alpha (gamma, K=5) = 32.22404
rate: 0.76648 0.89973 0.98989 1.08606 1.25784
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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