--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 18 17:30:30 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/285/Kdm2-PB/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/285/Kdm2-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-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/285/Kdm2-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -15096.74 -15111.64 2 -15095.61 -15112.36 -------------------------------------- TOTAL -15096.03 -15112.06 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/285/Kdm2-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-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/285/Kdm2-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} 1.349686 0.002688 1.251258 1.452087 1.348476 1395.45 1448.23 1.001 r(A<->C){all} 0.101127 0.000084 0.083596 0.119610 0.100825 888.01 988.98 1.002 r(A<->G){all} 0.216299 0.000174 0.190926 0.242217 0.215987 996.42 1021.34 1.000 r(A<->T){all} 0.122610 0.000154 0.100925 0.148442 0.122445 999.64 1029.37 1.001 r(C<->G){all} 0.042169 0.000024 0.033055 0.051616 0.041961 860.43 1024.55 1.000 r(C<->T){all} 0.454089 0.000312 0.418655 0.487784 0.454149 934.56 944.51 1.001 r(G<->T){all} 0.063706 0.000048 0.050133 0.077389 0.063396 1041.40 1117.29 1.000 pi(A){all} 0.215468 0.000034 0.204509 0.226715 0.215424 930.65 1002.12 1.000 pi(C){all} 0.284435 0.000038 0.272841 0.296385 0.284336 880.48 937.04 1.000 pi(G){all} 0.310504 0.000045 0.297046 0.323221 0.310322 835.69 865.60 1.000 pi(T){all} 0.189594 0.000029 0.178657 0.199653 0.189523 842.08 911.02 1.000 alpha{1,2} 0.124026 0.000037 0.112893 0.136609 0.123853 1126.84 1201.48 1.000 alpha{3} 6.466085 1.465477 4.263936 8.901446 6.353301 1258.08 1379.54 1.000 pinvar{all} 0.271561 0.000409 0.231396 0.311446 0.271754 1173.05 1237.87 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 -13495.123407 Model 2: PositiveSelection -13495.123426 Model 0: one-ratio -13634.385871 Model 3: discrete -13474.623958 Model 7: beta -13477.695254 Model 8: beta&w>1 -13472.789692 Model 0 vs 1 278.52492800000255 Model 2 vs 1 3.80000019504223E-5 Model 8 vs 7 9.811123999999836 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_Kdm2-PB) Pr(w>1) post mean +- SE for w 581 S 0.536 0.833 583 G 0.988* 1.299 816 A 0.878 1.185 823 N 0.582 0.881 929 V 0.866 1.173 1032 S 0.933 1.242 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_Kdm2-PB) Pr(w>1) post mean +- SE for w 581 S 0.751 1.265 +- 0.420 583 G 0.975* 1.480 +- 0.126 586 P 0.737 1.243 +- 0.445 592 A 0.581 1.080 +- 0.514 600 G 0.688 1.206 +- 0.451 605 P 0.598 1.093 +- 0.516 816 A 0.871 1.390 +- 0.293 823 N 0.753 1.271 +- 0.412 929 V 0.891 1.406 +- 0.276 1032 S 0.937 1.448 +- 0.208