      5    319

1SZ2_A                          KYALVGDVGG TNARLALCDI ASGEISQAKT YSGLDYPSLE AVIRVYLEEH KVEVKDGCIA IACPITGDWV AMTNHTWAFS IAEMKKNLGF SHLEIINDFT AVSMAIPMLK KEHLIQFGGA EPVEGKPIAV YGAGTGLGVA HLVHVDKRWV SLPGEGGHVD FAPNSEEEAI ILEILRAEIG HVSAERVLSG PGLVNLYRAI VKADNRLPEN LKPKDITERA LADSCTDCRR ALSLFCVIMG RFGGNLALNL GTFGGVFIAG GIVPRFLEFF KASGFRAAFE DKGRFKEYVH DIPVYLIVHD NPGLLGSGAH LRQTLGHIL
GLK_ECO                         KYALVGDVGG TNARLALCDI ASGEISQAKT YSGLDYPSLE AVIRVYLEEH KVEVKDGCIA IACPITGDWV AMTNHTWAFS IAEMKKNLGF SHLEIINDFT AVSMAIPMLK KEHLIQFGGA EPVEGKPIAV YGAGTGLGVA HLVHVDKRWV SLPGEGGHVD FAPNSEEEAI ILEILRAEIG HVSAERVLSG PGLVNLYRAI VKADNRLPEN LKPKDITERA LADSCTDCRR ALSLFCVIMG RFGGNLALNL GTFGGVFIAG GIVPRFLEFF KASGFRAAFE DKGRFKEYVH DIPVYLIVHD NPGLLGSGAH LRQTLGHIL
I0ABJ0                          KYALVGDVGG TNARLALCDI ASGEISQAKT YSGLDYPSLE AVVRVYLDEH SVSVEDGCIA IACPITGDWV AMTNHTWAFS IAEMKKNLGF SHLEIINDFT AVSMAIPMLK KEHLIQFGGG EPVDGKPIAV YGAGTGLGVA HLVHVDKRWI SLPGEGGHVD FAPNSEEEAM ILEILRAEIG HVSAERVLSG PGLVNLYRAI VKSDNRLPEN LRPKDITERA LADNCIDCRR ALSLFCVIMG RFGGDLALTM GTYGGVYIAG GIVPRFLEFF KASGFRGGFE DKGRFKDYVH GIPVYLIVHD NPGLLGSGAH LRQTLGHIL
C9XXD4                          KYALVGDVGG TNARLALCDV DSGEILKAKT YSGLDYPSLE AVVRVYLKEH NATVTDGCIA IACPITGDWV AMTNHVWAFS VAEMKKNLGF DHLEIINDFT AVSMAIPMLK TDHLIQFGGG EAQPNKPIAV YGAGTGLGVA HLVHVDKRWV SLPGEGGHVD FAPNSEEEAI ILEQLRAEVG HVSAERVLSG PGLVNLYRAI VKADGRLPDN LRPKDITERA LDDSCTDCRR ALSLFCVIMG RFGGNLALTL GTFGGVYIAG GIVPRFLDFF TSSGFRGGFE DKGRFKTYVQ DIPVYLIVHD QPGLLGAGAH LRQTLGQIL
GLK_YER                         TYALVGDVGG TNARLALCAV ATGEILQAKT YSGLEYESLE DVIKQYLSEH QAKVTDACIA IACPITGDWV AMTNHTWAFS IAAMQQNLGL DHLEVINDFT AVSMAIPVLP AQDVLQFGGT QPQPGKPVAV YGAGTGLGVA HLVNVDRRWI SLAGEGGHVD FAPNSEEEDQ ILAVLRQELG HVSAERVLSG PGLVNLYRAI VISDARLPEK LAPKDITARA LADSCTDCRR ALSLFCVIMG RFGGNLALNL STFGGVYIAG GIVPRFMEFF KASGFRAAFE DKGRFKDFLQ DIPVYMITHP QPGLLGAGAY LRQKLGYEL



Printing out site pattern counts


         5         98  P

1SZ2_A                          AAAAAAAACD DDDDEEEEEE EEEFFFFGGG GHHHHHHIII IIIIIIIKKK KKKKKKKKLL LLMMNNNNNN PPPPQQRRSS SSSSTTTTVV VVVVVWYY
GLK_ECO                         AAAAAAAACD DDDDEEEEEE EEEFFFFGGG GHHHHHHIII IIIIIIIKKK KKKKKKKKLL LLMMNNNNNN PPPPQQRRSS SSSSTTTTVV VVVVVWYY
I0ABJ0                          AAAAAGGSCD DDDGDDDEEE EESFFYYGGG GHHHHHHIII IIIIIMVEKK KKKKKKRSLL LMMMDNNNNT PPPPQQRRNS SSSSITTTIV VVVVVWYY
C9XXD4                          AAADSGGACD DDDDKPTDDE EETFFFYGGG NHHHHQQIII IQVVVIVTKK KKKKTTRNLL LLMMNGNNQT APPPKQRRSA DLSSTTTVVA QVVVVWYY
GLK_YER                         ADQAAATSCA DEPDSPDEQA EQKFLFYAGS GDHNYQYEIL VVILVQITIK PQRTAKAQLM VLMVNAKNQN PAEPQQKRSA DLSTTKTTIA QLQTVWFY



   22    2    1    2    1    2    1    1    6    1   11    1    1    1    1
    1    1    2    1    3   11    1    1   12    1    1    1    1   32    1
    1    1    7    1    1    1    1    1   14    1    2    1    1    1    1
    1    1    1    1    5    1    2    1    1    1    1    1    1   29    2
    1    1    4    1    1    1    1    6    1    1    1    1    1   10    1
    2    1   14    1    1    1    1   10    1    1    1    8    1    1    1
    1    1    1    1   19    3    1    7

AAML (in paml version 4.8, March 2014)  Glucokinases_Aln_Tree.nex
Model: Empirical for branches,  (GlobalMatrixProt_Evol.dat) ns =   5  ls = 319


Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
1SZ2_A                         0.10031 0.04702 0.03448 0.04702 0.01881 0.00940 0.06897 0.10972 0.03762 0.07524 0.10345 0.05016 0.01567 0.04702 0.04075 0.04702 0.03448 0.00940 0.02508 0.07837
GLK_ECO                        0.10031 0.04702 0.03448 0.04702 0.01881 0.00940 0.06897 0.10972 0.03762 0.07524 0.10345 0.05016 0.01567 0.04702 0.04075 0.04702 0.03448 0.00940 0.02508 0.07837
I0ABJ0                         0.08777 0.05016 0.03135 0.05643 0.01881 0.00940 0.05956 0.12226 0.03762 0.07524 0.10031 0.04075 0.02194 0.04075 0.04075 0.05329 0.03448 0.00940 0.03135 0.07837
C9XXD4                         0.09091 0.05016 0.03135 0.06583 0.01881 0.02194 0.04702 0.11912 0.03135 0.05956 0.10658 0.04075 0.01567 0.04389 0.04075 0.04075 0.05016 0.00940 0.02821 0.08777
GLK_YER                        0.11912 0.04702 0.02821 0.05329 0.01881 0.04389 0.05016 0.10345 0.02194 0.05643 0.10972 0.03135 0.01881 0.04389 0.04389 0.04389 0.04702 0.00940 0.03135 0.07837

Homogeneity statistic: X2 = 0.09899 G = 0.09331 

Average                        0.09969 0.04828 0.03197 0.05392 0.01881 0.01881 0.05893 0.11285 0.03323 0.06834 0.10470 0.04263 0.01755 0.04451 0.04138 0.04639 0.04013 0.00940 0.02821 0.08025

# constant sites:    232 (72.73%)
ln Lmax (unconstrained) = -1207.421893

AA distances (raw proportions of different sites)

1SZ2_A         
GLK_ECO          0.0000
I0ABJ0           0.0690  0.0690
C9XXD4           0.1191  0.1191  0.1254
GLK_YER          0.2069  0.2069  0.2257  0.2194


TREE #  1:  ((2, (3, (4, 5))), 1);   MP score: 111
This is a rooted tree.  Please check!
lnL(ntime:  8  np:  8):  -1513.368752      +0.000000
   6..7     7..2     7..8     8..3     8..9     9..4     9..5     6..1  
 0.000000 0.000000 0.026964 0.043948 0.042896 0.062773 0.190296 0.000000

tree length =   0.36688

((2: 0.000000, (3: 0.043948, (4: 0.062773, 5: 0.190296): 0.042896): 0.026964): 0.000000, 1: 0.000000);

((GLK_ECO: 0.000000, (I0ABJ0: 0.043948, (C9XXD4: 0.062773, GLK_YER: 0.190296): 0.042896): 0.026964): 0.000000, 1SZ2_A: 0.000000);

Time used:  0:00
