--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Nov 10 20:13:51 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/191/CG8312-PD/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/191/CG8312-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/191/CG8312-PD/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/191/CG8312-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -9100.91 -9115.02 2 -9101.31 -9118.79 -------------------------------------- TOTAL -9101.09 -9118.12 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/191/CG8312-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/191/CG8312-PD/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/191/CG8312-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.797077 0.001625 0.722786 0.878671 0.796476 1341.39 1413.75 1.000 r(A<->C){all} 0.085494 0.000107 0.064824 0.104911 0.085072 969.31 1013.03 1.000 r(A<->G){all} 0.191701 0.000281 0.159075 0.223364 0.191427 539.31 694.32 1.000 r(A<->T){all} 0.106973 0.000273 0.072901 0.137356 0.106186 860.64 890.34 1.000 r(C<->G){all} 0.071433 0.000058 0.056759 0.086149 0.071125 1033.79 1267.39 1.000 r(C<->T){all} 0.452768 0.000578 0.409154 0.502105 0.452253 480.84 697.16 1.000 r(G<->T){all} 0.091632 0.000139 0.069458 0.114947 0.091190 948.39 1023.22 1.000 pi(A){all} 0.243465 0.000063 0.227275 0.258086 0.243431 952.97 971.59 1.000 pi(C){all} 0.298010 0.000069 0.280605 0.313285 0.297862 952.51 1098.64 1.000 pi(G){all} 0.309037 0.000069 0.292199 0.324522 0.308945 1123.14 1201.38 1.000 pi(T){all} 0.149488 0.000038 0.137241 0.161231 0.149356 990.23 1009.51 1.000 alpha{1,2} 0.164367 0.000231 0.136108 0.194366 0.163483 1422.03 1426.49 1.000 alpha{3} 4.105226 1.014065 2.299863 6.057803 3.970267 1163.42 1264.19 1.000 pinvar{all} 0.326143 0.001158 0.262434 0.395479 0.327615 798.48 1040.58 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 -7979.277444 Model 2: PositiveSelection -7979.277444 Model 0: one-ratio -8091.814581 Model 3: discrete -7953.774753 Model 7: beta -7960.734676 Model 8: beta&w>1 -7954.139605 Model 0 vs 1 225.0742739999987 Model 2 vs 1 0.0 Model 8 vs 7 13.190141999999469 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_CG8312-PD) Pr(w>1) post mean +- SE for w 9 S 0.921 1.616 13 D 0.996** 1.720 48 V 0.758 1.388 93 A 0.925 1.621 587 T 0.767 1.403 667 A 0.940 1.643 831 T 0.596 1.164 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_CG8312-PD) Pr(w>1) post mean +- SE for w 9 S 0.934 1.448 +- 0.232 13 D 0.981* 1.491 +- 0.128 48 V 0.868 1.381 +- 0.334 52 A 0.625 1.093 +- 0.556 93 A 0.928 1.444 +- 0.234 96 T 0.681 1.183 +- 0.490 97 T 0.591 1.087 +- 0.522 98 A 0.625 1.126 +- 0.509 483 S 0.663 1.183 +- 0.465 587 T 0.851 1.374 +- 0.325 634 T 0.526 1.037 +- 0.511 667 A 0.926 1.444 +- 0.231 831 T 0.775 1.301 +- 0.390 832 S 0.730 1.216 +- 0.497