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BASEML (in paml version 4.6, August 2012) Alignments/alignment.phylip F84 dGamma (ncatG=5)
Nonhomo: 4 fix_kappa 0
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: 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): -320.224923 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.000716 0.000710 0.000004 0.000982 4.900290 5.049651 4.181698 7.779250 8.219953 5.399855 1.257356 0.270017 0.256473 0.242881 0.000316 0.508459 0.481713 0.594066 0.000094 0.399435 0.245435 0.262865 0.254539 0.000020 0.048763 0.942828 0.202387 0.161944 0.370189 0.265012 0.246425 0.265971 0.254134 0.235185 0.276679 2.390385
tree length = 0.00242
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.000716): 0.000004, Gorilla_go: 0.000710): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.000982);
Detailed output identifying parameters
kappa under F84 (in order of branches): 4.90029 5.04965 4.18170 7.77925 8.21995 5.39985 1.25736
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.27002 0.25647 0.24288 0.23063 )
Node #2 ( 0.00032 0.50846 0.48171 0.00951 )
Node #3 ( 0.59407 0.00009 0.39943 0.00641 )
Node #4 ( 0.24543 0.26287 0.25454 0.23716 )
Node #5 ( 0.00002 0.04876 0.94283 0.00839 )
Node #6 ( 0.20239 0.16194 0.37019 0.26548 )
Node #7 ( 0.26501 0.24643 0.26597 0.22259 )
Node #8 ( 0.25413 0.23518 0.27668 0.23400 )
Note: node 6 is root.
alpha (gamma, K=5) = 2.39039
rate: 0.29699 0.59017 0.86746 1.22435 2.02103
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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