--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Nov 12 00:45:34 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-PD/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/2/Abl-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PD/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-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -14935.82 -14951.49 2 -14936.37 -14953.09 -------------------------------------- TOTAL -14936.06 -14952.58 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/2/Abl-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PD/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-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.787466 0.001051 0.723095 0.849453 0.786687 1477.98 1482.74 1.000 r(A<->C){all} 0.081350 0.000066 0.065749 0.097226 0.081102 1085.96 1091.11 1.000 r(A<->G){all} 0.237455 0.000222 0.206450 0.264577 0.237114 919.23 952.55 1.000 r(A<->T){all} 0.164295 0.000241 0.133557 0.194215 0.163796 901.91 947.13 1.000 r(C<->G){all} 0.040937 0.000022 0.031787 0.050197 0.040800 986.75 1134.80 1.001 r(C<->T){all} 0.379734 0.000345 0.342372 0.414997 0.379931 748.04 778.55 1.000 r(G<->T){all} 0.096229 0.000106 0.076887 0.116455 0.095942 1124.49 1143.98 1.000 pi(A){all} 0.232558 0.000034 0.220998 0.243320 0.232601 969.00 1052.30 1.000 pi(C){all} 0.320617 0.000039 0.308509 0.332443 0.320471 996.34 1052.06 1.001 pi(G){all} 0.284757 0.000040 0.271639 0.296079 0.284628 967.66 1072.69 1.000 pi(T){all} 0.162068 0.000024 0.152608 0.171882 0.161850 929.90 996.92 1.000 alpha{1,2} 0.130354 0.000076 0.112894 0.147104 0.130179 1382.96 1414.86 1.000 alpha{3} 6.611760 1.625309 4.265224 9.180761 6.486721 1311.35 1406.18 1.000 pinvar{all} 0.378240 0.000455 0.339652 0.423048 0.377980 1209.64 1325.05 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 -13576.935707 Model 2: PositiveSelection -13576.935708 Model 0: one-ratio -13704.788551 Model 3: discrete -13568.334719 Model 7: beta -13568.905111 Model 8: beta&w>1 -13568.541213 Model 0 vs 1 255.7056879999982 Model 2 vs 1 2.0000006770715117E-6 Model 8 vs 7 0.7277959999992163
>C1 MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP TVGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASL LADAAELQQHQQDSGGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAP GPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDS GNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESE SSPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVP HEGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQY GEVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIG VCTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSY LESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPI KWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPAIDLTDVYHKLD KGYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSIT EAVEKQLNANATSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLS LTPQMVKKGLPGGQALTPNAHHNDPHQQQASTPMSETGSTSTKLSTFSSQ GKGNVQMRRTTNKQGKQAPAPPKRTSLLSSSRDSTYREEDPANARCNFID DLSTNGIHKLKTANYFSQTLSRNFKTQIPTHHTHQIRTQQQQQQQSVQQQ QQIVPLSVQQQAHQQQQKQQQYSIKKSSSCSSFLYDILFRGLARDINSLT QRYDSETDPAADPDTDATGDSLEQSLSQVIAAPVTNKMQHSLHSGGGGGG IGPRSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQLHSQAPGPGPPSTQP HHGNNGVVTSAHPITVGALDVMNVKQVVNRYGTLPKGARIGAYLDSLEDS SEAAPALPATAPSLPPANGHATPPAARLNPKASPIPPQQMIRSNSSGGVT MQNNAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGVASGVQ PALANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPN NGNISNGNGTNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSS LGSPPEDLKEKLITEIKAAGKDTAPASHLANGSGIAVVDPVSLLVTELAE SMNLPKPPPQQQQKLTNGNSTGSGFKAQLKKVEPKKMSAPMPKAEPANTI IDFKAHLRRVDKEKEPATPAPAPATVAVANNANCNTTGTLNRKEDGSKKF SQAMQKTEIKIDVTNSNVEADAGAAGEGDLGKRRSTDDEEQSHTEGLGSG GQGSADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKLTEPASSASS TQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNILHNSCVIFAE NGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLVAEVGQSLRQ ISNALNRooooooooooooooooooooooo >C2 MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP TVGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASL LADAAELQQHQQDSGGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAP GPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDS GNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESE SSPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVP HEGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQY GEVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIG VCTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSY LESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPI KWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPGIDLTDVYHKLE KGYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSIT EAVEKQLNANATSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLS LTPQMVKKGLSGGQSLTPNAHHNDPHQQQASTPMSETGSTSTKLSTFSSQ GKGNVQMRRTTNKQGKQAPAPPKRTSLLSSSRDSTYREEDPANARCNFID DLSTNGIHKLKTANYFSQTLSRNFKTQIPTQHTHQIRTQQQQQQQSVQQQ QQTVPLSVQQQPHQQQKQQQYSIKKSSSCSSFLYDILFRGLARDINSLTQ RYDSETDPAGDPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGI GPRSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPQAPGPGPPSTQPH HGNNGVLTSAHPITVGALEVMNVKQVVNRYGTLPKGARIGAYLDSLEDST EAAPPLPATAPSLPPANGHATPPSARLNPKASPIPPQQMIRSNSSGGVTM QNNAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGLASGVQP ALANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNN GNISNGNGSNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSSL GSPPEDLKEKLITEIKAAGKESAPASHLANGSGIAVVDPVSLLVTELAES MNLPKSPPQQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPMPKAEPASTII DFKAHLRRVDKEKEPAAPAPAPVAVANNANCNTTGTLNRKEDSSKKFSQA MQKTEIKIDVTNSNVEADAGATGEGDLGKRRSTDDEEQSHTEGLGSGGQG AADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKLTEPASSASSTQI SRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNILHNSCVIFAENGA MPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLVAEVGQSLRQISN ALNRoooooooooooooooooooooooooo >C3 MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVNSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGSGSGLSQRSGGHKDARCNPT VGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASLL ADAAELQQHQQDSGGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAPG PEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDSG NVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESES SPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVPH EGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYG EVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGV CTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSYL ESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPIK WTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPGIDLTDVYHKLEK GYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSITE AVEKQLNANATSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLSL TPQMVKKGLPGGQSLTPNAHHNDSHQQQASTPMSETGSTSTKLSTFSSQG KGNVQMRRTTNKQGKQAPAPPKRTSLLSSSRDSTYREEDPATARCNFIDD LSTNGIHKLKTANYFSQTLSRNFKTQIPTHHTHQIRTQLQQQQSVQQQTV PLPVQQQQPQHQKQKQQQYSIKKSSSCSSFLYDILFRGLARDINSLTQRY DSETDPAADPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGIGP RSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPLAPGPGPPATQPHHG NNGVVASAHPITVGALEVMNVKQVVNRYGTLPKVARIGAYLDSLEDSTEA APALPATAPALPPANGHATPPAARINPKASPIPPQQMIRSNSSGGVTMQN NAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRNATGAASGVQPAL ANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGN ISNGNGTNNNDSSHNDVSNTAPSVEEASSRFGVSLRKREPSTDSCSSLGS PPEDLKEKLITEIKAAGKDSAPASQLANGSGIAVVDPVSLLVTELAESMN LPKPPPQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPIAKAEPANTIIDFK AHLRRVDKEKEPAAPAPAPVAVTNNANCNTTGTLNRKEDSSKKFSQAMQK TEIKIDVTNSNVEADAGAAGEGDLGKRRSTDDEEQSHSDGLGSGGQGAAD MTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKLAEPASSASSTQISRD SILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNILHNSCVIFAENGAMPP HSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLVAEVGQSLRQISNALN Rooooooooooooooooooooooooooooo >C4 MGAQQGKDRGGHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP TVGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASL LADAAELQQHQQDSSGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAP GPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDS GNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESE SSPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVP HEGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQY GEVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIG VCTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSY LESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPI KWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPGIDLTDVYHKLE KGYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHM