--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 25 20:35:49 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/1/5PtaseI-PB/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/5PtaseI-PB/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/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4082.08 -4102.10 2 -4081.66 -4100.16 -------------------------------------- TOTAL -4081.85 -4101.55 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/5PtaseI-PB/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/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.792332 0.003858 0.674209 0.915036 0.791070 1360.41 1430.71 1.000 r(A<->C){all} 0.092136 0.000236 0.065148 0.124305 0.091030 994.10 1084.55 1.000 r(A<->G){all} 0.277879 0.000960 0.220915 0.339648 0.276815 775.02 1024.41 1.000 r(A<->T){all} 0.077631 0.000216 0.049040 0.106012 0.076891 831.03 998.86 1.000 r(C<->G){all} 0.103459 0.000282 0.072710 0.136586 0.102804 931.28 1041.02 1.000 r(C<->T){all} 0.395887 0.001073 0.329778 0.457849 0.395170 785.07 922.60 1.000 r(G<->T){all} 0.053009 0.000176 0.027774 0.079523 0.052377 1022.31 1153.44 1.000 pi(A){all} 0.280606 0.000141 0.256989 0.303160 0.280586 937.38 1063.64 1.000 pi(C){all} 0.241643 0.000127 0.220478 0.263679 0.241417 822.03 1057.65 1.000 pi(G){all} 0.229851 0.000131 0.208545 0.252974 0.229730 946.33 962.57 1.002 pi(T){all} 0.247900 0.000129 0.223819 0.268950 0.247951 1058.51 1169.56 1.000 alpha{1,2} 0.150232 0.000394 0.113824 0.189729 0.148777 1232.59 1325.92 1.000 alpha{3} 2.881911 0.663871 1.421088 4.459782 2.775990 1274.78 1350.86 1.000 pinvar{all} 0.378688 0.002217 0.290828 0.473814 0.381450 1321.93 1333.48 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 -3580.847241 Model 2: PositiveSelection -3580.847254 Model 0: one-ratio -3621.141036 Model 3: discrete -3576.040902 Model 7: beta -3576.743784 Model 8: beta&w>1 -3576.512053 Model 0 vs 1 80.58759000000009 Model 2 vs 1 2.5999999706982635E-5 Model 8 vs 7 0.4634619999997085
>C1 MESAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAVAQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVNEIIQSDDWTYGMIGEAVCMGDHKVLRIPQLYRSYRRAWRTW >C2 MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLNEFLAKIAVAQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENVKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVNEIIQSDDWTYGMIGEAVCMGDHKALRIPQLYRSYRRAWRTW >C3 MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIARAQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVNEIIQGDDWTYGMIGEAVCMGDHKALRIPQLSRSYRRAWRTW >C4 MDSAQEDASCTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAHAQPRFL GLHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVNEIIQSDDWTYGMIGEAVCMGDHKALRIPQLSRSYRRAWRTW >C5 MDSAQEEDSCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVTSLKIWNFLTHSWEESLQDIQDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVHEIIRSDDWTYGMIGEAVCMGDHKAPRIPLVLPSCRRAWRTW >C6 MDTAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKIAHVQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVHEIIRSDDWTYGMIGESVCMGDHKoooooooooooooooooo >C7 MDSAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVQEIIRSDDWTYGMIGEAVCMGDHKoooooooooooooooooo >C8 MDSAQEDGSCTDIFLVTANVGSLFEDPERLLQLWLNEFLAKISHVQPRFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVHEIIRGDDWTYGMIGEGVCMGDHKALQIPLVFPNYRRAWRTW >C9 MDSAQEDGSGTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISQVAPKFL ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPELADFTCVHIFMDEDFKSAE HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK ELTENLTAHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVHEIIRSDDWKYGMIGEAVCMGDHKALRIPPAFRSYRKLWRTW >C10 MDSAQEDGSSTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL ALHLQEVGGKTYEKSMEYVQEFIKCLCDSPELADFTCVHIFMDEDFKSAE HFTALGSLYFVHQDVASLKIWNFLTHNWEESLQDTKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDILVEYPIMFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVQEIIRSDDWTYGMIGEAVCMGDHKALRIPPAFRSCRRAWRTW >C11 MDSAQEDGVCTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL ALHLQEVGGKTYEKSMEYVQEFIKCLCDAPEMAQFTCVHIFMDEDFKSAE HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT KEKSKFPQHFFPECKWSRKGFMRTRWEVNGTVIDLVNIHLFHDASNLAAC ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE DWLKKFDRELEPLKDILVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD RILMSPQVHEIIRSDDWTYGMIGEAVCMGDHKALQIPPEYQSCRRAWQTW CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE: ], CPU=0.00 sec, SCORE=100, Nseq=11, Len=400 C1 MESAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAVAQPRFL C2 MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLNEFLAKIAVAQPRFL C3 MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIARAQPRFL C4 MDSAQEDASCTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAHAQPRFL C5 MDSAQEEDSCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL C6 MDTAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKIAHVQPRFL C7 MDSAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL C8 MDSAQEDGSCTDIFLVTANVGSLFEDPERLLQLWLNEFLAKISHVQPRFL C9 MDSAQEDGSGTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISQVAPKFL C10 MDSAQEDGSSTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL C11 MDSAQEDGVCTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL *::***: **:********************** ******: . *:** C1 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE C2 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE C3 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE C4 GLHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE C5 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE C6 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE C7 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE C8 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE C9 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPELADFTCVHIFMDEDFKSAE C10 ALHLQEVGGKTYEKSMEYVQEFIKCLCDSPELADFTCVHIFMDEDFKSAE C11 ALHLQEVGGKTYEKSMEYVQEFIKCLCDAPEMAQFTCVHIFMDEDFKSAE .**********************:****:**:.:**************** C1 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT C2 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT C3 HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT C4 HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT C5 HFTALGSLYFVHKDVTSLKIWNFLTHSWEESLQDIQDKHIYSGNIETIAT C6 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT C7 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT C8 HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT C9 HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT C10 HFTALGSLYFVHQDVASLKIWNFLTHNWEESLQDTKDKHIYSGNIETIAT C11 HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT ************:** **********.******* :************** C1 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C2 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C3 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C4 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C5 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C6 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C7 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C8 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C9 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C10 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC C11 KEKSKFPQHFFPECKWSRKGFMRTRWEVNGTVIDLVNIHLFHDASNLAAC ***************************:********************** C1 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C2 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C3 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C4 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C5 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C6 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C7 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C8 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C9 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK C10 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK C11 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK **********************************:*************** C1 ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE C2 ELTENLTPHRVQNVKNENVKIHYR