--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Nov 21 14:03:34 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/3/ACC-PB/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/3/ACC-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-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/3/ACC-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -26622.08 -26643.25 2 -26623.77 -26641.26 -------------------------------------- TOTAL -26622.61 -26642.68 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/3/ACC-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/3/ACC-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/3/ACC-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} 1.572864 0.001844 1.487657 1.654629 1.571973 1320.81 1410.90 1.000 r(A<->C){all} 0.082497 0.000034 0.070955 0.093833 0.082220 910.52 1002.91 1.000 r(A<->G){all} 0.314054 0.000131 0.293011 0.336018 0.313619 866.74 894.03 1.000 r(A<->T){all} 0.113188 0.000077 0.094955 0.129599 0.113062 983.01 1050.30 1.000 r(C<->G){all} 0.042194 0.000011 0.035776 0.048369 0.042126 1113.83 1118.42 1.000 r(C<->T){all} 0.385143 0.000142 0.360243 0.406597 0.385129 801.07 873.93 1.000 r(G<->T){all} 0.062924 0.000025 0.053481 0.072691 0.062688 1064.02 1098.75 1.001 pi(A){all} 0.210983 0.000020 0.201901 0.219119 0.211025 927.85 939.39 1.000 pi(C){all} 0.290154 0.000023 0.280085 0.299172 0.290047 918.93 1002.66 1.000 pi(G){all} 0.284796 0.000024 0.275630 0.294350 0.284856 882.53 912.29 1.000 pi(T){all} 0.214067 0.000019 0.204823 0.221968 0.214157 737.54 779.36 1.000 alpha{1,2} 0.091150 0.000009 0.085180 0.097121 0.091079 1231.52 1253.72 1.000 alpha{3} 7.805217 1.491383 5.679169 10.356290 7.679660 1336.24 1418.62 1.000 pinvar{all} 0.292626 0.000197 0.266299 0.321154 0.292798 1303.99 1368.61 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 -24565.66932 Model 0: one-ratio -24706.841833 Model 3: discrete -24513.827021 Model 7: beta -24531.162579 Model 8: beta&w>1 -24523.020721 Model 0 vs 1 282.34505799999897 Model 2 vs 1 3.2000003557186574E-5 Model 8 vs 7 16.283715999998094 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-PB) 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