
seed used = 552599837


Data set 1
      5    285

human                            VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY RLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFGDLSTP DAVMGNPKVK AHGKKVLGAF SDGLAHLDNL KGTFATLSEL HCDKLHVDPE NFRLLGNVLV CVLAHHFGKE FTPPVQAAYQ KVVAGVANAL AHKYH
goat-cow                         VLSAADKSNV KAAWGKVGGN AGAYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGE KVAAALTKAV GHLDDLPGTL SDLSDLHAHK LRVDPVNFKL LSHSLLVTLA CHLPNDFTPA VHASLDKFLA NVSTVLTSKY RLTAEEKAAV TAFWGKVKVD EVGGEALGRL LVVYPWTQRF FESFGDLSTA DAVMNNPKVK AHGKKVLDSF SNGMKHLDDL KGTFAALSEL HCDKLHVDPE NFKLLGNVLV VVLARNFGKE FTPVLQADFQ KVVAGVANAL AHRYH
rabbit                           VLSPADKTNI KTAWEKIGSH GGEYGAEAVE RMFLGFPTTK TYFPHFDFTH GSEQIKAHGK KVSEALTKAV GHLDDLPGAL STLSDLHAHK LRVDPVNFKL LSHCLLVTLA NHHPSEFTPA VHASLDKFLA NVSTVLTSKY RLSSEEKSAV TALWGKVNVE EVGGEALGRL LVVYPWTQRF FESFGDLSSA NAVMNNPKVK AHGKKVLAAF SEGLSHLDNL KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV IVLSHHFGKE FTPQVQAAYQ KVVAGVANAL AHKYH
rat                              VLSADDKTNI KNCWGKIGGH GGEYGEEALQ RMFAAFPTTK TYFSHIDVSP GSAQVKAHGK KVADALAKAA DHVEDLPGAL STLSDLHAHK LRVDPVNFKF LSHCLLVTLA CHHPGDFTPA MHASLDKFLA SVSTVLTSKY RLTDAEKAAV NALWGKVNPD DVGGEALGRL LVVYPWTQRY FDSFGDLSSA SAIMGNPKVK AHGKKVINAF NDGLKHLDNL KGTFAHLSEL HCDKLHVDPE NFRLLGNMIV IVLGHHLGKE FTPCAQAAFQ KVVAGVASAL AHKYH
marsupial                        VLSDADKTHV KAIWGKVGGH AGAYAAEALA RTFLSFPTTK TYFPHFDLSP GSAQIQGHGK KVADALSQAV AHLDDLPGTM SKLSDLHAHK LRVDPVNFKL LSHCLIVTLA AHLSKDLTPE VHASMDKFFA SVATVLTSKY RLTSEEKNCI TTIWSKVQVD QTGGEALGRM LVVYPWTTRF FGSFGDLSSP GAVMSNSKVQ AHGAKVLTSF GEAVKHLDNL KGTYAKLSEL HCDKLHVDPE NFKMLGNIIV ICLAEHFGKD FTPECQVAWQ KLVAGVAHAL AHKYH



Printing out site pattern counts


         5        126  P

human                            VLSPADKTNV AAWGGAHAEY GAEALERMFL SPTPHFLSHA QVKGKADTNV AVDMNALANL CLALPAEFAV LSSTPESAVT ALGNVDEVQF ETPDVMGKLG ASDLANFTCR VLCVAHFEPV AAYVNK
goat-cow                         VLSAADKSNV AAWGGGNAAY GAEALERMFL SPTPHFLSHA QVKGEAATKV GLDLGTLDNL SLCLPNDFAV LNSTAEAAVT AFGKVDEVQF ETADVMNKLD SSNMKDFACK VLVVARFEVL ADFVNR
rabbit                           VLSPADKTNI TAWEGSHGEY GAEAVERMFL GPTPHFFTHE QIKAKSETKV GLDLGALTNL CLNHPSEFAV LNSSSESAVT ALGNVEEVQF ESANVMNKLA ASELSNFKCR VLIVSHFEQV AAYVNK
rat                              VLSADDKTNI NCWGGGHGEY GEEALQRMFA APTSHIVSPA QVKAKADAKA DVELGALTNF CLCHPGDFAM LSSTDAAAVN ALGNPDDVQY DSASIMGKIN ANDLKNFHCR MIIVGHLECA AAFVSK
marsupial                        VLSDADKTHV AIWGGGHAAY AAEALARTFL SPTPHFLSPA QIQGKADSQV ALDLGTMKNL CIALSKDLEV FSATSENCIT TISQVDQTTF GSPGVMSALT SGEVKNYKCK IIICAEFDEC VAWLHK



   16   21   10    1    1   10   17    1    1    2    1    1    3    1   13
    1    2    1    1    5    2    1    5   15    1    1    5    1   10    1
    1    7   10    1   14    1    1    1    1    1    3    1    2    1    1
    1    1    1    1    1    1    1    1    1    1    1    4    1    4    1
    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
    1    1    1    1    1    1

AAML (in paml version 4, June 2007)    ./test/material/codeml/abglobin.aa   Model: EqualInput dGamma (ncatG=8) ns =   5  ls = 285


Frequencies..
                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
human                          0.1263 0.0211 0.0351 0.0526 0.0105 0.0140 0.0421 0.0702 0.0632 0.0000 0.1263 0.0772 0.0105 0.0526 0.0491 0.0561 0.0561 0.0105 0.0211 0.1053
goat-cow                       0.1193 0.0246 0.0421 0.0632 0.0070 0.0140 0.0386 0.0737 0.0526 0.0000 0.1298 0.0842 0.0105 0.0596 0.0351 0.0596 0.0526 0.0105 0.0175 0.1053
rabbit                         0.0982 0.0211 0.0421 0.0386 0.0070 0.0175 0.0596 0.0702 0.0667 0.0140 0.1228 0.0842 0.0070 0.0561 0.0386 0.0737 0.0561 0.0105 0.0211 0.0947
rat                            0.1193 0.0211 0.0386 0.0667 0.0175 0.0175 0.0316 0.0807 0.0667 0.0246 0.1123 0.0842 0.0140 0.0491 0.0386 0.0596 0.0456 0.0105 0.0211 0.0807
marsupial                      0.1088 0.0175 0.0211 0.0561 0.0175 0.0281 0.0351 0.0702 0.0632 0.0281 0.1088 0.0842 0.0175 0.0491 0.0351 0.0737 0.0667 0.0140 0.0211 0.0842

Homogeneity statistic: X2 = 0.13569 G = 0.15654 

Average                        0.114386 0.021053 0.035789 0.055439 0.011930 0.018246 0.041404 0.072982 0.062456 0.013333 0.120000 0.082807 0.011930 0.053333 0.039298 0.064561 0.055439 0.011228 0.020351 0.094035

# constant sites:    170 (59.65%)
ln Lmax (unconstrained) = -1189.106658


TREE #  1:  (((3, 4), 1), 2, 5);   MP score: 177
lnL(ntime:  7  np:  8):  -1817.465211     +0.000000
   6..7     7..8     8..3     8..4     7..1     6..2     6..5  
 0.033639 0.038008 0.082889 0.187866 0.055050 0.096992 0.284574 0.588710

tree length =   0.77902

(((3: 0.082889, 4: 0.187866): 0.038008, 1: 0.055050): 0.033639, 2: 0.096992, 5: 0.284574);

(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);

Detailed output identifying parameters

alpha (gamma, K = 8) =  0.58871
rate:   0.01357  0.09006  0.22445  0.42476  0.71414  1.14510  1.85916  3.52875
freq:   0.12500  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500

Time used:  0:01


Data set 2
