      5    419

1EY2_A                          AELKYISGFG NECSSEDPRC PGSLPEGQNN PQVCPYNLYA EQLSGSAFTC PRSTNKRSWL YRILPSVSHK PFESIDEGHV THNWDEVDPD PNQLRWKPFE IPKASQKKVD FVSGLHTLCG AGDIKSNNGL AIHIFLCNTS MENRCFYNSD GDFLIVPQKG NLLIYTEFGK MLVQPNEICV IQRGMRFSID VFEETRGYIL EVYGVHFELP DLGPIGANGL ANPRDFLIPI AWYEDRQVPG GYTVINKYQG KLFAAKQDVS PFNVVAWHGN YTPYKYNLKN FMVINSVAFD HADPSIFTVL TAKSVRPGVA IADFVIFPPR WGVADKTFRP PYYHRNCMSE FMGLIRGFLP GGGSLHSTMT PHGPDADCFE KASKVKLAPE RIADGTMAFM FESSLSLAVT KWGLKASRLK SHFTPNSRN
HGD_HUM                         AELKYISGFG NECSSEDPRC PGSLPEGQNN PQVCPYNLYA EQLSGSAFTC PRSTNKRSWL YRILPSVSHK PFESIDEGQV THNWDEVDPD PNQLRWKPFE IPKASQKKVD FVSGLHTLCG AGDIKSNNGL AIHIFLCNTS MENRCFYNSD GDFLIVPQKG NLLIYTEFGK MLVQPNEICV IQRGMRFSID VFEETRGYIL EVYGVHFELP DLGPIGANGL ANPRDFLIPI AWYEDRQVPG GYTVINKYQG KLFAAKQDVS PFNVVAWHGN YTPYKYNLKN FMVINSVAFD HADPSIFTVL TAKSVRPGVA IADFVIFPPR WGVADKTFRP PYYHRNCMSE FMGLIRGFLP GGGSLHSTMT PHGPDADCFE KASKVKLAPE RIADGTMAFM FESSLSLAVT KWGLKASRLK SHFTPNSRN
B8YB76_B                        TELKYISGFG NECASEDPRC PGALPEGQNN PQVCPYNLYA EQLSGSAFTC PRSTNKRSWL YRILPSVSHK PFEFIDQGHI THNWDEVDPD PNQLRWKPFE IPKASQKKVD FVNGLHTLCG AGDIRSNNGL AIHIFLCNTS MGNRCFYNSD GDLLIVPQKG KLLIYTEFGK MLVQPNEICV IQRGMRFSID VFEETRGYIL EVYGVHFELP DLGPIGANGL ANPRDFLIPV AWYEDRQVPG GYTVINKYQG KLFAAKQDVS PFNVVAWHGN YTPYKYNLEN FMVINSVAFD HADPSIFTVL TAKSVRPGVA IADFVIFPPR WGVADKTFRP PYYHRNCMSE FMGLIKGFLP GGGSLHSPMT PHGPDANCFE KASKAKLAPE RIADGTMAFM FESSLNIAVT KWGLKTSNLK SRFTPNSRN
HGD_MOU                         AELKYISGFG NECASEDPRC PGSLPKGQNN PQVCPYNLYA EQLSGSAFTC PRNTNKRSWL YRILPSVSHK PFESIDQGHV THNWDEVGPD PNQLRWKPFE IPKASEKKVD FVSGLYTLCG AGDIKSNNGL AVHIFLCNSS MENRCFYNSD GDFLIVPQKG KLLIYTEFGK MSLQPNEICV IQRGMRFSVD VFEETRGYIL EVYGVHFELP DLGPIGANGL ANPRDFLIPV AWYEDRRVPG GYTVINKFQG KLFACKQDVS PFNVVAWHGN YTPYKYNLEN FMVINAVAFD HADPSIFTVL TAKSLRPGVA IADFVIFPPR WGVADKTFRP PYYHRNCMSE FMGLIKGFLP GGGSLHSAMT PHGPDADCFE KASKAKLEPE RIADGTMAFM FESSLSLAVT KWGLKTCSLR SHFTPNSRS
Q6AYR0                          AELKYISGFG NECASEDPRC PGSLPKGQNN PQICPYNLYA EQLSGSAFTC PRNTNKRSWL YRILPSVSHK PFASIDQGHI NHNWDEVGPD PNQLRWKPFE IPKACQKKVD FVSGLHTLCG AGDIRSNNGL AVHIFLCNSP MENRCFYNSD GDFLIVPQKG KLLIYTEFGK MFLQPNEICV IQRGMRFSVD VFEETRGYIL EVYGVHFELP DLGPIGANGL ANPRDFLIPV AWYEDRQVPG GFTVINKYQG KLFASKQDVS PFNVVAWHGN YTPYKYNLEN FMVINAVAFD HADPSIFTVL TAKSLRPGVA IADFVIFPPR WGVADKTFRP PYYHRNCMSE FMGLIKGFLP GGGSLHSAMT PHGPDADCFE KASKAKLEPE RIADGTMAFM FESSLSLAVT KWGLKTCGLQ AHFTPTSRS



Printing out site pattern counts


         5         67  P

1EY2_A                          AAAAACDDDE EEEEFFGHHH HIIIKKKKLL LMNNNNPQQQ RRRSSSSSSS SSSSTTTTVV VVVWYYY
HGD_HUM                         AAAAACDDDE EEEEFFGHHH QIIIKKKKLL LMNNNNPQQQ RRRSSSSSSS SSSSTTTTVV VVVWYYY
B8YB76_B                        AAATTCDDNE EEGQFLGHHR HIIVEKKRIL LMKNNNPQQQ KNRAAFNSSS SSSSPTTTAI VVVWYYY
HGD_MOU                         ACEATCDGDE EKEQFFGHYH HIVVEKRKLL SMKNNSPEQR KSRASSSACN SSSSASTTAV LVVWFYY
Q6AYR0                          ASEATCDGDA EKEQFFGHHH HIVVEKQRLL FMKNTSPQQQ KGRASSSACN ACPSASNTAI LIVWYFY



   21    1    1    1    1   10   19    1    1    1   17    1    1    1   26
    1   33    9    1    1    1   20    2    1    1   20    1    1    1   29
    1    9    1   22    1    1   32    1    9    1    1    1   17    1    1
    1    2    1    1    1    1    1    1   20    1    1    1   14    1    1
    2    1   21    7    1    1   14

AAML (in paml version 4.8, March 2014)  Homogentisate_Aln_Tree.nex
Model: Empirical for branches,  (GlobalMatrixProt_Evol.dat) ns =   5  ls = 419


Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
1EY2_A                         0.05967 0.04535 0.05967 0.05012 0.02387 0.02625 0.05012 0.07876 0.02864 0.05489 0.07399 0.05489 0.02148 0.06444 0.07637 0.07399 0.04057 0.01671 0.03819 0.06205
HGD_HUM                        0.05967 0.04535 0.05967 0.05012 0.02387 0.02864 0.05012 0.07876 0.02625 0.05489 0.07399 0.05489 0.02148 0.06444 0.07637 0.07399 0.04057 0.01671 0.03819 0.06205
B8YB76_B                       0.06205 0.04535 0.06683 0.04773 0.02387 0.02864 0.04773 0.08115 0.02625 0.05728 0.07399 0.05489 0.02148 0.06444 0.07876 0.06205 0.04296 0.01671 0.03819 0.05967
HGD_MOU                        0.06205 0.04535 0.05728 0.04773 0.02864 0.02387 0.05251 0.08115 0.02625 0.04773 0.07637 0.05728 0.02148 0.06683 0.07637 0.07399 0.03819 0.01671 0.03819 0.06205
Q6AYR0                         0.06683 0.04296 0.05728 0.04773 0.02864 0.03103 0.04773 0.08353 0.02864 0.05251 0.07637 0.05489 0.02148 0.06921 0.07876 0.06444 0.03819 0.01671 0.03580 0.05728

Homogeneity statistic: X2 = 0.00908 G = 0.00909 

Average                        0.06205 0.04487 0.06014 0.04869 0.02578 0.02768 0.04964 0.08067 0.02721 0.05346 0.07494 0.05537 0.02148 0.06587 0.07733 0.06969 0.04010 0.01671 0.03771 0.06062

# constant sites:    369 (88.07%)
ln Lmax (unconstrained) = -1419.302347

AA distances (raw proportions of different sites)

1EY2_A         
HGD_HUM          0.0024
B8YB76_B         0.0525  0.0549
HGD_MOU          0.0692  0.0716  0.0788
Q6AYR0           0.0835  0.0859  0.0835  0.0430


TREE #  1:  ((2, (3, (4, 5))), 1);   MP score: 58
This is a rooted tree.  Please check!
lnL(ntime:  8  np:  8):  -1588.202824      +0.000000
   6..7     7..2     7..8     8..3     8..9     9..4     9..5     6..1  
 0.000000 0.002246 0.022660 0.029948 0.035239 0.015790 0.027504 0.000000

tree length =   0.13339

((2: 0.002246, (3: 0.029948, (4: 0.015790, 5: 0.027504): 0.035239): 0.022660): 0.000000, 1: 0.000000);

((HGD_HUM: 0.002246, (B8YB76_B: 0.029948, (HGD_MOU: 0.015790, Q6AYR0: 0.027504): 0.035239): 0.022660): 0.000000, 1EY2_A: 0.000000);

Time used:  0:00
