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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
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