--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 11 22:55:39 WET 2016 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/2/Abl-PA/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -15110.38 -15129.90 2 -15110.60 -15126.07 -------------------------------------- TOTAL -15110.48 -15129.23 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.824864 0.001191 0.764090 0.900067 0.823901 1355.93 1428.47 1.000 r(A<->C){all} 0.080029 0.000063 0.065827 0.096519 0.079969 855.08 968.46 1.000 r(A<->G){all} 0.242900 0.000235 0.213529 0.273674 0.242324 817.99 889.51 1.000 r(A<->T){all} 0.164673 0.000243 0.134402 0.194552 0.164115 1000.79 1006.32 1.003 r(C<->G){all} 0.035059 0.000018 0.026764 0.043025 0.034931 1319.24 1323.85 1.000 r(C<->T){all} 0.381759 0.000340 0.344894 0.416450 0.381958 731.41 738.28 1.000 r(G<->T){all} 0.095579 0.000099 0.076502 0.115008 0.095383 842.60 954.21 1.002 pi(A){all} 0.224361 0.000032 0.213681 0.235634 0.224226 1017.12 1027.58 1.000 pi(C){all} 0.324495 0.000039 0.312512 0.337098 0.324372 897.39 917.82 1.000 pi(G){all} 0.291512 0.000039 0.279433 0.303503 0.291614 864.00 1010.08 1.000 pi(T){all} 0.159631 0.000022 0.150534 0.168617 0.159663 926.87 1017.94 1.001 alpha{1,2} 0.127424 0.000063 0.111068 0.141948 0.127338 1361.57 1400.88 1.000 alpha{3} 6.619604 1.566201 4.343072 9.157669 6.493033 1462.92 1481.96 1.000 pinvar{all} 0.376988 0.000417 0.336003 0.416148 0.377277 1183.71 1185.43 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -13690.531085 Model 2: PositiveSelection -13690.531085 Model 0: one-ratio -13807.238424 Model 3: discrete -13682.842607 Model 7: beta -13685.517501 Model 8: beta&w>1 -13683.005896 Model 0 vs 1 233.41467799999737 Model 2 vs 1 0.0 Model 8 vs 7 5.023209999999381
>C1 MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP TVGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSGGLG LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG NLLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLV GDNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSD VWAFGVLLWEIATYGMSPYPAIDLTDVYHKLDKGYRMERPPGCPPEVYDL MRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSA PSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQALTP NAHHNDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQA PAPPKRTSLLSSSRDSTYREEDPANARCNFIDDLSTNGLARDINSLTQRY DSETDPAADPDTDATGDSLEQSLSQVIAAPVTNKMQHSLHSGGGGGGIGP RSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQLHSQAPGPGPPSTQPHHG NNGVVTSAHPITVGALDVMNVKQVVNRYGTLPKGARIGAYLDSLEDSSEA APALPATAPSLPPANGHATPPAARLNPKASPIPPQQMIRSNSSGGVTMQN NAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGVASGVQPAL ANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGN ISNGNGTNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSSLGS PPEDLKEKLITEIKAAGKDTAPASHLANGSGIAVVDPVSLLVTELAESMN LPKPPPQQQQKLTNGNSTGSGFKAQLKKVEPKKMSAPMPKAEPANTIIDF KAHLRRVDKEKEPATPAPAPATVAVANNANCNTTGTLNRKEDGSKKFSQA MQKTEIKIDVTNSNVEADAGAAGEGDLGKRRSTGSINSLKKLWEQQPPAP DYATSTILQQQPSVVNGGGTPNAQLSPKYGMKSGAINTVGTLPAKLGNKQ PPAAPPPPPPNCTTSNSSTTSISTSSRDCTSRQQASSTIKTSHSTQLFTD DEEQSHTEGLGSGGQGSADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATP IAKLTEPASSASSTQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDK LNILHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDN ERLVAEVGQSLRQISNALNRooooooooooooooooo >C2 MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP TVGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSGGLG LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG NLLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLV GDNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSD VWAFGVLLWEIATYGMSPYPGIDLTDVYHKLEKGYRMERPPGCPPEVYDL MRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSA PSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLSGGQSLTP NAHHNDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQA PAPPKRTSLLSSSRDSTYREEDPANARCNFIDDLSTNGLARDINSLTQRY DSETDPAGDPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGIGP RSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPQAPGPGPPSTQPHHG NNGVLTSAHPITVGALEVMNVKQVVNRYGTLPKGARIGAYLDSLEDSTEA APPLPATAPSLPPANGHATPPSARLNPKASPIPPQQMIRSNSSGGVTMQN NAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGLASGVQPAL ANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGN ISNGNGSNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSSLGS PPEDLKEKLITEIKAAGKESAPASHLANGSGIAVVDPVSLLVTELAESMN LPKSPPQQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPMPKAEPASTIIDF KAHLRRVDKEKEPAAPAPAPVAVANNANCNTTGTLNRKEDSSKKFSQAMQ KTEIKIDVTNSNVEADAGATGEGDLGKRRSTGSINSLKKLWEQQPPASDY ATSTILQQQPVVNGGGTQTAQLSPKYGMKSGAINTAGTLPAKLGNKPPPA APPPPPPNCTTSNSSTTSISTSSRDCTSRQQASSTIKTSHSTQLFADDEE QSHTEGLGSGGQGAADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAK LTEPASSASSTQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNI LHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERL VAEVGQSLRQISNALNRoooooooooooooooooooo >C3 MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVNSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGSGSGLSQRSGGHKDARCNPT VGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSGGLGL QGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQAG GENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLEK HSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHY RISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQNK PTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVKT LKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHGN LLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLVG DNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSDV WAFGVLLWEIATYGMSPYPGIDLTDVYHKLEKGYRMERPPGCPPEVYDLM RQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSAP STSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQSLTPN AHHNDSHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQAP APPKRTSLLSSSRDSTYREEDPATARCNFIDDLSTNGLARDINSLTQRYD SETDPAADPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGIGPR SSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPLAPGPGPPATQPHHGN NGVVASAHPITVGALEVMNVKQVVNRYGTLPKVARIGAYLDSLEDSTEAA PALPATAPALPPANGHATPPAARINPKASPIPPQQMIRSNSSGGVTMQNN AAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRNATGAASGVQPALA NLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGNI SNGNGTNNNDSSHNDVSNTAPSVEEASSRFGVSLRKREPSTDSCSSLGSP PEDLKEKLITEIKAAGKDSAPASQLANGSGIAVVDPVSLLVTELAESMNL PKPPPQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPIAKAEPANTIIDFKA HLRRVDKEKEPAAPAPAPVAVTNNANCNTTGTLNRKEDSSKKFSQAMQKT EIKIDVTNSNVEADAGAAGEGDLGKRRSTGSINSLKKLWEQQPPAPDYAT STILQQQPSVVNGGGTPNAQLSPKYGMKSGAPNTGGTLPAKLGNKPPPAA PPPPPPNCTTSNLSTTSISTSSRDCTSRQQASSTIKTSHSTQLFTDDEEQ SHSDGLGSGGQGAADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKL AEPASSASSTQISRDSILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNIL HNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLV AEVGQSLRQISNALNRooooooooooooooooooooo >C4 MGAQQGKDRGGHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP TVGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSSGLG LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG NLLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLV GDNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSD VWAFGVLLWEIATYGMSPYPGIDLTDVYHKLEKGYRMERPPGCPPEVYDL MRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSA PSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQSLTP NAHHTDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQA PAPPKRTSLLSSSRDSTYREEDPATARCNFIDDLSTNGFARDINSLTQRY DSETDPAADPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGIGPR SSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPLAPGPGPPATQPHHGN NGVVTSAHPITVGALEVMNVKQVVNRYGTLPKGARIGAYLDSLEDSSEAA PALPATAPSLPPANGHATPPAARINPKASPIPPQQMIRSNSSGGVTMQNN AAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSATGVASGVQPALA NLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGNI SNGNGTNNNDSSHNDVSNTAPSVEEASSRFGVSLRKREPSTDSCSSLGSP PEDLKEKLITEIKASGKDSAPTSHLANGSGIAVVDPVSQLFTELEESMKL PKPPPQQQKLTNGNGTGSGFKAQLKKVEPKKMCAPMAKAEPANTIIDFKA HLRRVDKEKEPAAPAPAPVPAAAPVAVTNNANCNTTGTLNRKEDSSKKFS QVMQKTEIKIDVTNSNVEADAGAAGEGDLGKRRSTGSINSLKKLWEQQPP APDYATSTILQQQPSVVNGGGTPNAQLSPKYGMKSGATNAGGTLPAKLGN KPPPAAPPPPPPNCTTSNLSTTSISTSSRDFTSRQQASSTIKTSHSTQLF TDDEEQSHSDGLGSGGQGAADMTQSLYEQKPQIQQKPVVPHKPTKLTIYA TPIAKLAEPASSTQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKL NILHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNE RLVAEVGQSLRQISNALNRoooooooooooooooooo >C5 MGAQQGKDRGAHSGGGGSAAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVVSGGGSGGGGGGSGSGLSQRSGGHKDPRCNP SVGLNIFTEHNEALLQSRPLPHIPAGSAAASLLADAAEMQQHQQDSGGLG LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG NLLD