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BASEML (in paml version 4.5, December 2011) 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 0.2009 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: 39): -320.124168 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.000365 0.000335 0.000004 0.000443 5.000031 4.994267 5.000106 9.848190 10.187031 5.000028 1.472416 0.259141 0.251000 0.258787 0.000256 0.785552 0.209323 0.807849 0.000150 0.188802 0.253502 0.255880 0.250493 0.000008 0.025018 0.971770 0.202711 0.162552 0.369861 0.241017 0.273417 0.249272 0.252420 0.409219 0.074412 3.035652
tree length = 0.00116
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.000004, Pan_troglo: 0.000365): 0.000004, Gorilla_go: 0.000335): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.000443);
Detailed output identifying parameters
kappa under F84 (in order of branches): 5.00003 4.99427 5.00011 9.84819 10.18703 5.00003 1.47242
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.25914 0.25100 0.25879 0.23107 )
Node #2 ( 0.00026 0.78555 0.20932 0.00487 )
Node #3 ( 0.80785 0.00015 0.18880 0.00320 )
Node #4 ( 0.25350 0.25588 0.25049 0.24013 )
Node #5 ( 0.00001 0.02502 0.97177 0.00320 )
Node #6 ( 0.20271 0.16255 0.36986 0.26488 )
Node #7 ( 0.24102 0.27342 0.24927 0.23629 )
Node #8 ( 0.25242 0.40922 0.07441 0.26395 )
Note: node 6 is root.
alpha (gamma, K=5) = 3.03565
rate: 0.35336 0.63986 0.89490 1.21288 1.89900
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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