--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Nov 21 16:35:44 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/3/ACC-PC/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-PC/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/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -26623.68 -26641.93 2 -26623.79 -26642.60 -------------------------------------- TOTAL -26623.73 -26642.32 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-PC/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/3/ACC-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.573264 0.001804 1.495471 1.659774 1.572764 1354.62 1356.66 1.000 r(A<->C){all} 0.082248 0.000034 0.070621 0.093093 0.082331 879.11 1009.85 1.000 r(A<->G){all} 0.313411 0.000132 0.290646 0.335403 0.313446 767.11 920.42 1.000 r(A<->T){all} 0.113105 0.000075 0.096776 0.130174 0.113066 642.98 772.00 1.000 r(C<->G){all} 0.042181 0.000011 0.035286 0.048481 0.042094 959.19 1042.12 1.000 r(C<->T){all} 0.385873 0.000146 0.362370 0.410283 0.385761 678.31 699.49 1.000 r(G<->T){all} 0.063181 0.000024 0.053665 0.072696 0.063027 972.68 1011.42 1.000 pi(A){all} 0.211309 0.000022 0.202558 0.220713 0.211353 873.30 942.37 1.000 pi(C){all} 0.290136 0.000022 0.280997 0.299088 0.290063 1043.83 1177.90 1.000 pi(G){all} 0.284877 0.000024 0.275321 0.294607 0.284679 870.20 904.41 1.001 pi(T){all} 0.213678 0.000019 0.205192 0.222091 0.213596 531.25 806.71 1.002 alpha{1,2} 0.091149 0.000010 0.085312 0.097479 0.091061 1385.04 1443.02 1.000 alpha{3} 7.809226 1.477869 5.665973 10.377980 7.690800 1313.49 1397.25 1.000 pinvar{all} 0.292115 0.000180 0.265606 0.318286 0.292330 1086.92 1188.77 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 -24565.669304 Model 2: PositiveSelection -24565.669356 Model 0: one-ratio -24706.841833 Model 3: discrete -24514.70771 Model 7: beta -24531.162641 Model 8: beta&w>1 -24523.020789 Model 0 vs 1 282.34505799999897 Model 2 vs 1 1.0399999882793054E-4 Model 8 vs 7 16.283704000001308 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_ACC-PC) Pr(w>1) post mean +- SE for w 280 N 0.655 1.196 +- 0.433 752 S 0.734 1.265 +- 0.410 757 Y 0.563 1.079 +- 0.499 815 L 0.692 1.220 +- 0.437 2136 A 0.515 1.026 +- 0.510