1 2seed used = 1024367525 3 4BASEML (in paml version 4.4c, August 2010) Alignments/alignment.phylip K80 dGamma (ncatG=5) 5Frequencies.. 6 T C A G 7Homo_sapie 0.2027 0.1622 0.3694 0.2658 8Pan_troglo 0.1982 0.1667 0.3694 0.2658 9Gorilla_go 0.2072 0.1577 0.3694 0.2658 10Pongo_pygm 0.2027 0.1622 0.3694 0.2658 11Macaca_mul 0.1937 0.1667 0.3739 0.2658 12 13Homogeneity statistic: X2 = 0.00092 G = 0.00092 14 15Average 0.2009 0.1631 0.3703 0.2658 16 17# constant sites: 218 (98.20%) 18ln Lmax (unconstrained) = -316.049385 19 20Distances: K80 (kappa) (alpha set at 0.50) 21This matrix is not used in later m.l. analysis. 22 23Homo_sapie 24Pan_troglo 0.0046(999.0000) 25Gorilla_go 0.0046(999.0000) 0.0093(999.0000) 26Pongo_pygm 0.0000(999.0000) 0.0046(999.0000) 0.0046(999.0000) 27Macaca_mul 0.0092( 2.0206) 0.0139( 4.1043) 0.0139( 4.1043) 0.0092( 2.0206) 28 29TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00 30lnL(ntime: 7 np: 9): -334.912612 +0.000000 31 6..7 7..8 8..1 8..2 7..3 6..4 6..5 32 0.000004 0.000004 0.000004 0.004516 0.004518 0.000004 0.009091 6.038381 999.000000 33 34tree length = 0.01814 35 36(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul); 37 38(((Homo_sapie: 0.000004, Pan_troglo: 0.004516): 0.000004, Gorilla_go: 0.004518): 0.000004, Pongo_pygm: 0.000004, Macaca_mul: 0.009091); 39 40Detailed output identifying parameters 41 42Parameters (kappa) in the rate matrix (K80) (Yang 1994 J Mol Evol 39:105-111): 43 6.03838 44 45alpha (gamma, K=5) = 999.00000 46rate: 0.95611 0.98294 0.99967 1.01660 1.04468 47freq: 0.20000 0.20000 0.20000 0.20000 0.20000 48 49check convergence.. 50