--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Dec 05 04:50:20 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/350/Pkcdelta-PD/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/350/Pkcdelta-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/350/Pkcdelta-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/350/Pkcdelta-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -6576.55 -6593.52 2 -6576.33 -6592.04 -------------------------------------- TOTAL -6576.43 -6593.03 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/350/Pkcdelta-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/350/Pkcdelta-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/350/Pkcdelta-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} 0.849595 0.003104 0.742248 0.957958 0.848366 1501.00 1501.00 1.000 r(A<->C){all} 0.092845 0.000169 0.067428 0.116894 0.092627 926.55 972.43 1.001 r(A<->G){all} 0.253404 0.000560 0.209904 0.301807 0.253111 938.31 964.52 1.000 r(A<->T){all} 0.088228 0.000191 0.062667 0.116073 0.087559 1171.71 1255.36 1.001 r(C<->G){all} 0.070279 0.000107 0.049981 0.090456 0.069668 1110.03 1157.75 1.001 r(C<->T){all} 0.443401 0.000719 0.390469 0.494819 0.443581 851.58 892.80 1.000 r(G<->T){all} 0.051843 0.000096 0.033483 0.071309 0.051249 1139.83 1218.34 1.000 pi(A){all} 0.249619 0.000088 0.230472 0.267183 0.249773 689.22 895.59 1.000 pi(C){all} 0.257112 0.000082 0.240067 0.275247 0.256987 1051.67 1119.47 1.002 pi(G){all} 0.266289 0.000090 0.248112 0.285533 0.266008 1089.92 1092.40 1.000 pi(T){all} 0.226981 0.000073 0.209805 0.243088 0.226804 1045.59 1125.84 1.001 alpha{1,2} 0.144474 0.000154 0.122032 0.169346 0.143691 1277.35 1307.53 1.001 alpha{3} 4.356708 1.059276 2.619300 6.501671 4.242129 1147.51 1309.29 1.000 pinvar{all} 0.497666 0.000636 0.448356 0.545667 0.498477 1308.08 1328.07 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 -5982.71707 Model 2: PositiveSelection -5982.717136 Model 0: one-ratio -6011.633126 Model 3: discrete -5975.812449 Model 7: beta -5979.246239 Model 8: beta&w>1 -5976.0363 Model 0 vs 1 57.83211200000005 Model 2 vs 1 1.320000010309741E-4 Model 8 vs 7 6.419878000000608 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_Pkcdelta-PD) Pr(w>1) post mean +- SE for w 96 V 0.935 1.709 98 I 0.974* 1.771 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_Pkcdelta-PD) Pr(w>1) post mean +- SE for w 96 V 0.903 1.507 +- 0.461 98 I 0.940 1.550 +- 0.451