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BASEML (in paml version 4.6, August 2012) Alignments/alignment.phylip F84 dGamma (ncatG=5)
Nonhomo: 3 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: 36): -320.028080 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.002240 0.001601 0.000004 0.000297 4.967404 4.921218 5.504625 64.179405 70.802178 5.718726 1.320007 0.271290 0.214061 0.288334 0.000001 0.081626 0.787480 0.005262 0.000000 0.913508 0.255013 0.233511 0.288538 0.000000 0.020108 0.979522 0.334191 0.153650 0.303990 0.203457 0.161982 0.369560 16.783993
tree length = 0.00415
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.002240): 0.000004, Gorilla_go: 0.001601): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.000297);
Detailed output identifying parameters
kappa under F84 (in order of branches): 4.96740 4.92122 5.50463 64.17941 70.80218 5.71873 1.32001
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.27129 0.21406 0.28833 0.22631 )
Node #2 ( 0.00000 0.08163 0.78748 0.13089 )
Node #3 ( 0.00526 0.00000 0.91351 0.08123 )
Node #4 ( 0.25501 0.23351 0.28854 0.22294 )
Node #5 ( 0.00000 0.02011 0.97952 0.00037 )
Node #6 ( 0.20346 0.16198 0.36956 0.26500 )
Node #7 ( 0.33419 0.15365 0.30399 0.20817 )
Node #8 ( 0.33419 0.15365 0.30399 0.20817 )
Note: node 6 is root.
alpha (gamma, K=5) = 16.78399
rate: 0.68404 0.85798 0.98063 1.11479 1.36257
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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