      5    465

1Z10_A                          KGKLPPGPTP LPFIGNYLQL NTEQMYNSLM KISERYGPVF TIHLGPRRVV VLCGHDAVRE ALVDQAEEFS GRGEQATFDW VFKGYGVVFS NGERAKQLRR FSIATLRDFG VGKRGIEERI QEEAGFLIDA LRGTGGANID PTFFLSRTVS NVISSIVFGD RFDYKDKEFL SLLRMMLGIF QFTSTSTGQL YEMFSSVMKH LPGPQQQAFQ LLQGLEDFIA KKVEHNQRTL DPNSPRDFID SFLIRMQEEE KNPNTEFYLK NLVMTTLNLF IGGTETVSTT LRYGFLLLMK HPEVEAKVHE EIDRVIGKNR QPKFEDRAKM PYMEAVIHEI QRFGDVIPMS LARRVKKDTK FRDFFLPKGT EVYPMLGSVL RDPSFFSNPQ DFNPQHFLNE KGQFKKSDAF VPFSIGKRNC FGEGLARMEL FLFFTTVMQN FRLKSSQSPK DIDVSPKHVG FATIPRNYTM SFLPR
CP2A6_H                         KGKLPPGPTP LPFIGNYLQL NTEQMYNSLM KISERYGPVF TIHLGPRRVV VLCGHDAVRE ALVDQAEEFS GRGEQATFDW VFKGYGVVFS NGERAKQLRR FSIATLRDFG VGKRGIEERI QEEAGFLIDA LRGTGGANID PTFFLSRTVS NVISSIVFGD RFDYKDKEFL SLLRMMLGIF QFTSTSTGQL YEMFSSVMKH LPGPQQQAFQ LLQGLEDFIA KKVEHNQRTL DPNSPRDFID SFLIRMQEEE KNPNTEFYLK NLVMTTLNLF IGGTETVSTT LRYGFLLLMK HPEVEAKVHE EIDRVIGKNR QPKFEDRAKM PYMEAVIHEI QRFGDVIPMS LARRVKKDTK FRDFFLPKGT EVFPMLGSVL RDPSFFSNPQ DFNPQHFLNE KGQFKKSDAF VPFSIGKRNC FGEGLARMEL FLFFTTVMQN FRLKSSQSPK DIDVSPKHVG FATIPRNYTM SFLPR
Q307K8                          GGKLPPGPTP LPFIGNYLQL NTEQMYNSLM KISERYGPVF TIHLGPRPVV VLCGHEAVKE ALVDQAEEFS GRGEQATFDW LFKGYGVAFS NGERAKQLRR FSITTLRDFG VGKRGIEERI QEEAGFLIEA LRGTRGAFID PTFFLSRTVS NVISSIVFGD RFDYEDKEFL SLLRMMLGSF QFTATSMGQL YEMFYSVMKH LPGPQQQAFK ELQGLEDFIT KKVEQNQRTL DPNSPRDFID SFLIRMQEEQ NNPNTEFYLK NLVLTTLNLF FAGTETVSTT LRYGFLLLMK HPDVEAKVHE EIDRVIGKNR QPKFEDRAKM PYTEAVIHEI QRFGDMIPMG VARRVIKDTK FREFLLPKGT EVFPMLGSVL RDAKFFSNPQ DFHPQHFLDE KGQFKKSDAF VPFSIGKRYC FGEGLARMEL FLFLTTILQN FHFKSPQLPQ DIDVSPKHVG FATIPRNYTM SFQPR
Q8SQ68                          QGKLPPGPTP LPFIGNYLQL NTEQMYNSLM KISQRYGPVF TVHLGPRRIV VLCGYDAVKE ALVDQAEEFS GRGEQATFDW LFKGYGVAFS NGERAKQLRR FSITTLRDFG VGKRGIEERI QEEAGYLIEA FRGTRGAFID PTYFLSRTVS NVISSIVFGD RFDYEDKEFL ALLRMMLGSF QFTATSTGQL YEMFYSVMKH LPGPQQQAFK DLQGLEDFIA RKVEHNQRTL DPNSPRDFID SFLIRMQEEK KNPDTEFYWK NLVLTTLNLF FAGTETVSTT MRYGFLLLMK HPDVEAKVHE EIDRVIGRNR QAKFEDRAKM PYTEAVIHEI QRFGDMIPMG LARRVTKDTK FRDFLLPKGT EVFPMLGSVL RDPKFFSNPR GFNPQHFLDE NGQFKKNDAF VPFSIGKRYC FGEGLARMEL FLFLTNILQN FHLKSPQLPQ DIDVSPKHVG FATIPPTYTM SFQPR
CP2A5_M                         SGKLPPGPTP LPFIGNFLQL NTEQMYNSLM KISQRYGPVF TIYLGPRRIV VLCGQEAVKE ALVDQAEEFS GRGEQATFDW LFKGYGVVFS SGERAKQLRR FSIATLRDFG VGKRGIEERI QEEAGFLIDS FRKTNGAFID PTFYLSRTVS NVISSIVFGD RFDYEDKEFL SLLRMMLGSF QFTATSMGQL YEMFSSVMKH LPGPQQQAFK ELQGLEDFIT KKVEHNQRTL DPNSPRDFID SFLIRMLEEK KNPNTEFYMK NLVLTTLNLF FAGTETVSTT LRYGFLLLMK HPDIEAKVHE EIDRVIGRNR QPKYEDRMKM PYTEAVIHEI QRFADMIPMG LARRVTKDTK FRDFLLPKGT EVFPMLGSVL KDPKFFSNPK DFNPKHFLDD KGQFKKNDAF VPFSIGKRYC FGEGLARMEL FLFLTNIMQN FHFKSTQAPQ DIDVSPRLVG FATIPPTYTM SFLSR



Printing out site pattern counts


         5        102  P

1Z10_A                          AAAAACDDDD DEEEEEFFFF GGGGGHHHHH IIIIKKKKKK KKKKLLLLLL LLMMMMNNNN NNNNPPPPQQ QQQRRRRRRS SSSSSSSSTT TVVVVVVVWY YY
CP2A6_H                         AAAAACDDDD DEEEEEFFFF GGGGGHHHHH IIIIKKKKKK KKKKLLLLLL LLMMMMNNNN NNNNPPPPQQ QQQRRRRRRS SSSSSSSSTT TVVVVVVVWF YY
Q307K8                          AAATTCDDEE EDEEEQFFFL AGGGRHHHHQ FIISEGIKKK KKNQEFLLLL QVLLMTDFHN NNNYAPPPKQ QQQHKPRRRA GKLPSSSYMT TAILMVVVWF YY
Q8SQ68                          AAAATCDGDD EDEEQKFFYL AGGGRHHHYH FIVSEQTKKN RRKQDLFLMW QLLLMTDFND NNTYPAPPKQ QQRHKRPRRA GKLPANSYTN TAILMIVVWF YY
CP2A5_M                         AMSTACDDDE DDDEQKFYFL AAGKNHLYQH FIISESTKRK KRKQEFFLLM LLLMMTDFNN NSTYPPPSKK LQKHKRPKRA GKATSNSSMN TVILMIIVWF FY



   14    1    1    1    1    2   19    1    1    1    1    1    1   27    1
    1   37    2    2    2    1    1   31    1    1    5    1    1    1    1
    1   20    1    1    1    1    1   20    1    1    1    1    1    1    1
    1    1   35    1    1    1    1    1    1   13    1    1    1    1    1
   12    1    1    1    1    1   24    1    1    1    1   18    1    1    1
    1    1    1   27    1    1    1    1    1    1    1   20    1    1    1
   23    1    1    1    1    1    1   23    1    1    1    9

AAML (in paml version 4.8, March 2014)  CytochromeP450_Aln_Tree.nex
Model: Empirical for branches,  (GlobalMatrixProt_Evol.dat) ns =   5  ls = 465


Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
1Z10_A                         0.03871 0.06882 0.04086 0.04946 0.00430 0.04731 0.06667 0.07527 0.01935 0.04946 0.09032 0.06237 0.03441 0.09247 0.05806 0.06022 0.05376 0.00215 0.02366 0.06237
CP2A6_H                        0.03871 0.06882 0.04086 0.04946 0.00430 0.04731 0.06667 0.07527 0.01935 0.04946 0.09032 0.06237 0.03441 0.09462 0.05806 0.06022 0.05376 0.00215 0.02151 0.06237
Q307K8                         0.04301 0.06452 0.03441 0.04731 0.00430 0.05376 0.07312 0.07527 0.02151 0.04946 0.09462 0.05806 0.03226 0.09677 0.06022 0.04946 0.05806 0.00215 0.02581 0.05591
Q8SQ68                         0.04731 0.07097 0.03656 0.05376 0.00430 0.05161 0.06452 0.07527 0.01935 0.04731 0.09247 0.05591 0.03226 0.09247 0.06022 0.04516 0.06022 0.00430 0.03226 0.05376
CP2A5_M                        0.04086 0.06452 0.03656 0.05376 0.00430 0.04516 0.06452 0.06882 0.01505 0.05161 0.09462 0.06667 0.03871 0.09677 0.05806 0.05806 0.06022 0.00215 0.02796 0.05161

Homogeneity statistic: X2 = 0.01928 G = 0.01915 

Average                        0.04172 0.06753 0.03785 0.05075 0.00430 0.04903 0.06710 0.07398 0.01892 0.04946 0.09247 0.06108 0.03441 0.09462 0.05892 0.05462 0.05720 0.00258 0.02624 0.05720

# constant sites:    380 (81.72%)
ln Lmax (unconstrained) = -1671.879048

AA distances (raw proportions of different sites)

1Z10_A         
CP2A6_H          0.0022
Q307K8           0.1011  0.0989
Q8SQ68           0.1226  0.1204  0.0774
CP2A5_M          0.1333  0.1312  0.1011  0.0968


TREE #  1:  ((2, ((4, 5), 3)), 1);   MP score: 106
This is a rooted tree.  Please check!
lnL(ntime:  8  np:  8):  -1968.399101      +0.000000
   6..7     7..2     7..8     8..9     9..4     9..5     8..3     6..1  
 0.000000 0.000000 0.081534 0.021289 0.038538 0.065489 0.024340 0.002092

tree length =   0.23328

((2: 0.000000, ((4: 0.038538, 5: 0.065489): 0.021289, 3: 0.024340): 0.081534): 0.000000, 1: 0.002092);

((CP2A6_H: 0.000000, ((Q8SQ68: 0.038538, CP2A5_M: 0.065489): 0.021289, Q307K8: 0.024340): 0.081534): 0.000000, 1Z10_A: 0.002092);

Time used:  0:00
