File: aa_pairwise-4_4c.out

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seed used = 1024005389
AAML (in paml version 4.4c, August 2010)  ../Alignments/aa_alignment.phylip
Model: Poisson for branchesns =   5  ls =  74


Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
Homo_sapie                     0.0000 0.0405 0.0270 0.0811 0.0405 0.0135 0.1622 0.0541 0.0000 0.0541 0.0946 0.1351 0.0405 0.0135 0.0541 0.0405 0.0270 0.0000 0.0135 0.1081
Pan_troglo                     0.0000 0.0405 0.0270 0.0811 0.0405 0.0135 0.1622 0.0541 0.0000 0.0541 0.0946 0.1351 0.0405 0.0135 0.0541 0.0405 0.0270 0.0000 0.0135 0.1081
Gorilla_go                     0.0000 0.0405 0.0270 0.0811 0.0405 0.0135 0.1622 0.0541 0.0000 0.0541 0.0946 0.1351 0.0405 0.0135 0.0541 0.0405 0.0270 0.0000 0.0135 0.1081
Pongo_pygm                     0.0000 0.0405 0.0270 0.0811 0.0405 0.0135 0.1622 0.0541 0.0000 0.0541 0.0946 0.1351 0.0405 0.0135 0.0541 0.0405 0.0270 0.0000 0.0135 0.1081
Macaca_mul                     0.0000 0.0405 0.0270 0.0811 0.0405 0.0135 0.1622 0.0541 0.0000 0.0541 0.0946 0.1351 0.0405 0.0135 0.0541 0.0405 0.0270 0.0000 0.0135 0.1081

Homogeneity statistic: X2 = 0.00000 G = 0.00000 

Average                         0.0000  0.0405  0.0270  0.0811  0.0405  0.0135  0.1622  0.0541  0.0000  0.0541  0.0946  0.1351  0.0405  0.0135  0.0541  0.0405  0.0270  0.0000  0.0135  0.1081

# constant sites:     74 (100.00%)
ln Lmax (unconstrained) = -192.057157

AA distances (raw proportions of different sites)

Homo_sapie     
Pan_troglo       0.0000
Gorilla_go       0.0000  0.0000
Pongo_pygm       0.0000  0.0000  0.0000
Macaca_mul       0.0000  0.0000  0.0000  0.0000


Printing out site pattern counts

         5          1  P

Homo_sapie                                 A
Pan_troglo                                 A
Gorilla_go                                 A
Pongo_pygm                                 A
Macaca_mul                                 A



   74


ML distances of aa seqs.
Homo_sapie     
Pan_troglo       0.0000
Gorilla_go       0.0000  0.0000
Pongo_pygm       0.0000  0.0000  0.0000
Macaca_mul       0.0000  0.0000  0.0000  0.0000