--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 18 20:20:39 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-PE/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/285/Kdm2-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-PE/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-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -15096.67 -15115.57 2 -15096.34 -15112.12 -------------------------------------- TOTAL -15096.49 -15114.91 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/285/Kdm2-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-PE/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-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.351250 0.002579 1.250763 1.450501 1.350649 1501.00 1501.00 1.000 r(A<->C){all} 0.100754 0.000081 0.083938 0.119266 0.100477 1122.44 1159.98 1.000 r(A<->G){all} 0.216724 0.000168 0.191735 0.241593 0.216321 877.24 977.79 1.001 r(A<->T){all} 0.122187 0.000145 0.099128 0.144804 0.122037 926.01 966.50 1.000 r(C<->G){all} 0.042427 0.000023 0.032886 0.051698 0.042265 1033.79 1041.79 1.000 r(C<->T){all} 0.454331 0.000292 0.420632 0.487794 0.454443 726.27 816.81 1.000 r(G<->T){all} 0.063578 0.000048 0.049908 0.076692 0.063453 1177.45 1179.67 1.000 pi(A){all} 0.215653 0.000035 0.205134 0.227951 0.215594 955.57 1039.09 1.000 pi(C){all} 0.284700 0.000039 0.273115 0.297309 0.284695 839.40 1040.34 1.001 pi(G){all} 0.310071 0.000047 0.296339 0.322642 0.310131 762.99 885.74 1.001 pi(T){all} 0.189575 0.000029 0.179854 0.200889 0.189476 984.44 1010.01 1.000 alpha{1,2} 0.123689 0.000039 0.112074 0.136279 0.123522 1111.33 1306.17 1.000 alpha{3} 6.449675 1.448376 4.354494 8.894667 6.311487 1325.40 1376.87 1.000 pinvar{all} 0.271480 0.000413 0.234253 0.313618 0.271817 1162.87 1214.20 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 -13495.123407 Model 0: one-ratio -13634.385871 Model 3: discrete -13472.075762 Model 7: beta -13477.695254 Model 8: beta&w>1 -13472.789692 Model 0 vs 1 278.52492800000255 Model 2 vs 1 0.0 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-PE) 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-PE) 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