      5    113

1SRN_A                          KETAAAKFER QHMDSSTSAA SSSNYCNQMM KSRNLTKDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGN
RNAS1_1                         KESRAKKFQR QHMDSDSSPS SSSTYCNQMM RRRNMTQGRC KPVNTFVHEP LVDVQNVCFQ EKVTCKNGQG NCYKSNSSMH ITDCRLTNGS RYPNCAYRTS PKERHIIVAC EGS
RNAS1_2                         KESPAMKFER QHMDSGSTSS SNPTYCNQMM KRRNMTQGWC KPVNTFVHEP LADVQAICLQ KNITCKNGQS NCYQSSSSMH ITDCRLTSGS KYPNCAYQTS QKERHIIVAC EGN
RNAS1_M                         RESAAQKFQR QHMDPDGSSI NSPTYCNQMM KRRDMTNGSC KPVNTFVHEP LADVQAVCSQ ENVTCKNRKS NCYKSSSALH ITDCHLKGNS KYPNCDYKTT QYQKHIIVAC EGN
RNS1B_R                         RESSADKFKR QHMDTEGPSK SSPTYCNQMM KRQGMTKGSC KPVNTFVHEP LEDVQAICSQ GQVTCKNGRN NCHKSSSTLR ITDCRLKGSS KYPNCDYTTT DSQKHIIIAC DGN



Printing out site pattern counts


         5         75  P

1SRN_A                          AAAAAAAAAA CDDEEEEFGG GHIKKKKKKK LLMMNNNNNN PQQQQRRRRS SSSSSSSSSS STTTTTTTVV VVYYY
RNAS1_1                         AAKKNPRSTV CDGEELQFGG NHIEKKQRRR LMMMEKNNST PKPQQRRRRD FGHPRSSSSS SGSSSSTTVV VVNYY
RNAS1_2                         AAKMASPSTA CDGEELEFGG SHIKKKQKQR LMMMENNNNT PQQQQRRRWG LGHPRNPSSS TSSSSSTTII VVSYY
RNAS1_M                         ADYQASAITA CDGEELQFGR GHIEKRNKKK LMLMQNDNNT PKQKQHRRSD SNHPRSPNPS SSAGSTKTVV VVSYY
RNS1B_R                         ADSDASSKTE CDGDELKFGG GHIGKRKKTK LMLMQQGNNT PKDRQRQRSE SSRPRSPSTS PNTGSTKTIV IVSHY



    2    1    1    1    1    1    1    1    1    1    8    3    1    1    2
    1    1    2    1    1    1    3    3    1    3    1    1    2    1    1
    1    1    1    3    1    1    1    5    1    1    2    1    1    1    4
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    3
    1    1    1    1    1    1    1    4    1    1    1    3    1    1    3


AAML (in paml version 4.8, March 2014)  PancreaticRibonucleases_Aln_Tree.nex
Model: Empirical for branches,  (GlobalMatrixProt_Evol.dat) ns =   5  ls = 113


Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
1SRN_A                         0.09735 0.03540 0.08850 0.03540 0.07080 0.06195 0.04425 0.02655 0.02655 0.02655 0.01770 0.08850 0.03540 0.01770 0.01770 0.12389 0.08850 0.00000 0.04425 0.05310
RNAS1_1                        0.02655 0.08850 0.07965 0.03540 0.07080 0.06195 0.04425 0.04425 0.03540 0.02655 0.01770 0.07080 0.04425 0.02655 0.04425 0.12389 0.06195 0.00000 0.03540 0.06195
RNAS1_2                        0.04425 0.04425 0.07965 0.02655 0.07080 0.07965 0.04425 0.04425 0.03540 0.04425 0.02655 0.07080 0.05310 0.01770 0.04425 0.12389 0.07080 0.00885 0.03540 0.03540
RNAS1_M                        0.05310 0.04425 0.08850 0.05310 0.07080 0.07080 0.03540 0.03540 0.04425 0.03540 0.02655 0.08850 0.03540 0.01770 0.04425 0.09735 0.06195 0.00000 0.04425 0.05310
RNS1B_R                        0.02655 0.05310 0.06195 0.06195 0.07080 0.06195 0.03540 0.06195 0.03540 0.04425 0.02655 0.09735 0.03540 0.01770 0.04425 0.11504 0.08850 0.00000 0.02655 0.03540

Homogeneity statistic: X2 = 0.26413 G = 0.25147 

Average                        0.04956 0.05310 0.07965 0.04248 0.07080 0.06726 0.04071 0.04248 0.03540 0.03540 0.02301 0.08319 0.04071 0.01947 0.03894 0.11681 0.07434 0.00177 0.03717 0.04779

# constant sites:     56 (49.56%)
ln Lmax (unconstrained) = -465.123580

AA distances (raw proportions of different sites)

1SRN_A         
RNAS1_1          0.3274
RNAS1_2          0.2920  0.2212
RNAS1_M          0.3186  0.3186  0.2920
RNS1B_R          0.3628  0.3805  0.3363  0.2478


TREE #  1:  (((2, 3), (4, 5)), 1);   MP score: 97
This is a rooted tree.  Please check!
lnL(ntime:  8  np:  8):   -821.586129      +0.000000
   6..7     7..8     8..2     8..3     7..9     9..4     9..5     6..1  
 0.106399 0.102522 0.162443 0.087616 0.117698 0.095750 0.206332 0.088987

tree length =   0.96775

(((2: 0.162443, 3: 0.087616): 0.102522, (4: 0.095750, 5: 0.206332): 0.117698): 0.106399, 1: 0.088987);

(((RNAS1_1: 0.162443, RNAS1_2: 0.087616): 0.102522, (RNAS1_M: 0.095750, RNS1B_R: 0.206332): 0.117698): 0.106399, 1SRN_A: 0.088987);

Time used:  0:01
