--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Dec 07 13:57:05 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/408/Sudx-PA/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PA/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/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -10162.07 -10179.24 2 -10162.69 -10181.17 -------------------------------------- TOTAL -10162.33 -10180.61 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PA/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/408/Sudx-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.282424 0.004054 1.155376 1.401699 1.278382 1238.64 1369.82 1.000 r(A<->C){all} 0.093619 0.000099 0.073675 0.111975 0.093537 864.36 941.50 1.001 r(A<->G){all} 0.285420 0.000342 0.249300 0.321306 0.285103 1055.63 1062.70 1.000 r(A<->T){all} 0.074786 0.000151 0.052861 0.100623 0.074104 873.86 910.56 1.000 r(C<->G){all} 0.036105 0.000031 0.025242 0.046710 0.035938 1081.87 1113.50 1.000 r(C<->T){all} 0.439101 0.000457 0.398411 0.481300 0.439469 880.89 909.47 1.000 r(G<->T){all} 0.070969 0.000084 0.053797 0.089608 0.070723 1111.97 1133.10 1.002 pi(A){all} 0.235698 0.000055 0.221536 0.250448 0.235660 676.27 921.50 1.000 pi(C){all} 0.283781 0.000061 0.268898 0.298724 0.283725 1032.40 1096.39 1.000 pi(G){all} 0.295730 0.000063 0.280527 0.311422 0.295661 1071.16 1111.11 1.000 pi(T){all} 0.184791 0.000041 0.172086 0.196821 0.184738 891.83 1027.14 1.000 alpha{1,2} 0.123388 0.000053 0.109698 0.137965 0.123154 1291.76 1396.38 1.000 alpha{3} 5.252987 1.154853 3.229533 7.345893 5.140676 1158.58 1172.33 1.000 pinvar{all} 0.375986 0.000472 0.334710 0.419216 0.376050 1344.00 1395.07 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 -9281.48237 Model 2: PositiveSelection -9281.482466 Model 0: one-ratio -9355.132281 Model 3: discrete -9266.787676 Model 7: beta -9268.495154 Model 8: beta&w>1 -9264.543014 Model 0 vs 1 147.29982200000086 Model 2 vs 1 1.919999995152466E-4 Model 8 vs 7 7.904279999998835 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_Sudx-PA) Pr(w>1) post mean +- SE for w 21 T 0.716 1.154 187 A 0.944 1.448 324 P 0.981* 1.494 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_Sudx-PA) Pr(w>1) post mean +- SE for w 21 T 0.794 1.326 +- 0.409 185 P 0.645 1.155 +- 0.514 187 A 0.912 1.446 +- 0.299 233 G 0.691 1.207 +- 0.495 322 G 0.657 1.168 +- 0.509 323 P 0.650 1.161 +- 0.512 324 P 0.956* 1.487 +- 0.244