--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Dec 09 16:29:26 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/423/Trpm-PJ/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/423/Trpm-PJ/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/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -16483.41 -16501.67 2 -16483.88 -16500.54 -------------------------------------- TOTAL -16483.62 -16501.25 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/423/Trpm-PJ/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/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.776225 0.001003 0.715548 0.838193 0.775973 1363.44 1432.22 1.001 r(A<->C){all} 0.084552 0.000068 0.069403 0.102197 0.084182 1168.68 1198.64 1.000 r(A<->G){all} 0.251603 0.000225 0.221670 0.280823 0.250993 1046.91 1079.77 1.000 r(A<->T){all} 0.110640 0.000164 0.086811 0.137402 0.110162 943.23 955.62 1.000 r(C<->G){all} 0.068055 0.000032 0.057814 0.079730 0.067865 1222.58 1258.69 1.000 r(C<->T){all} 0.426703 0.000326 0.392479 0.462222 0.426597 909.63 934.46 1.000 r(G<->T){all} 0.058448 0.000053 0.045274 0.073090 0.058232 1048.61 1140.32 1.000 pi(A){all} 0.214371 0.000029 0.203774 0.224580 0.214217 1150.07 1162.48 1.000 pi(C){all} 0.307492 0.000035 0.296584 0.319954 0.307543 976.58 1045.00 1.000 pi(G){all} 0.294482 0.000034 0.283248 0.305861 0.294467 836.50 940.96 1.000 pi(T){all} 0.183655 0.000024 0.173597 0.192283 0.183778 894.61 1044.80 1.000 alpha{1,2} 0.111514 0.000039 0.099867 0.123860 0.111289 1436.48 1467.15 1.000 alpha{3} 6.391538 1.423226 4.307163 8.832141 6.272657 1501.00 1501.00 1.000 pinvar{all} 0.505290 0.000254 0.474148 0.536118 0.505433 1209.31 1230.63 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 -15046.189274 Model 2: PositiveSelection -15046.189274 Model 0: one-ratio -15129.554409 Model 3: discrete -15035.537163 Model 7: beta -15039.068796 Model 8: beta&w>1 -15031.160836 Model 0 vs 1 166.73027000000002 Model 2 vs 1 0.0 Model 8 vs 7 15.815920000000915 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_Trpm-PJ) Pr(w>1) post mean +- SE for w 36 T 0.862 2.048 1233 G 0.800 1.915 1248 V 0.504 1.275 1451 I 0.993** 2.333 1456 A 0.988* 2.323 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_Trpm-PJ) Pr(w>1) post mean +- SE for w 36 T 0.875 1.402 +- 0.358 1233 G 0.850 1.377 +- 0.383 1234 P 0.695 1.209 +- 0.496 1248 V 0.740 1.259 +- 0.473 1451 I 0.953* 1.481 +- 0.241 1456 A 0.949 1.478 +- 0.251 1691 T 0.518 0.968 +- 0.600 1769 Q 0.694 1.210 +- 0.492