--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 03 21:02:43 WET 2017 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE 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= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S24/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/ADOPS1/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -7299.74 -7324.22 2 -7299.62 -7320.89 -------------------------------------- TOTAL -7299.68 -7323.56 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S24/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/ADOPS1/revmuscle/S24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.526172 0.003975 1.401025 1.646728 1.525765 1490.11 1495.55 1.000 r(A<->C){all} 0.119419 0.000141 0.097322 0.143094 0.118867 607.85 769.50 1.000 r(A<->G){all} 0.298933 0.000331 0.263852 0.334001 0.298466 858.48 869.35 1.000 r(A<->T){all} 0.074262 0.000057 0.060008 0.089341 0.073752 1055.82 1203.40 1.001 r(C<->G){all} 0.154746 0.000244 0.125397 0.185798 0.154099 829.69 890.90 1.000 r(C<->T){all} 0.267171 0.000302 0.233586 0.301605 0.266739 630.14 690.37 1.000 r(G<->T){all} 0.085468 0.000085 0.067959 0.103200 0.084985 842.46 960.21 1.000 pi(A){all} 0.293028 0.000116 0.272573 0.314161 0.293069 1065.70 1135.79 1.000 pi(C){all} 0.174873 0.000076 0.157566 0.191642 0.174665 1175.14 1176.77 1.000 pi(G){all} 0.196732 0.000086 0.179797 0.216285 0.196555 968.97 1078.30 1.000 pi(T){all} 0.335367 0.000132 0.311555 0.356059 0.335312 1036.07 1162.47 1.000 alpha{1,2} 0.763396 0.014241 0.566847 1.016668 0.747600 1099.68 1291.73 1.000 alpha{3} 2.360759 0.398417 1.274220 3.588140 2.256517 1233.25 1289.72 1.000 pinvar{all} 0.048625 0.001381 0.000029 0.118790 0.040283 1053.27 1192.57 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 -3367.119516 Model 2: PositiveSelection -3344.39726 Model 0: one-ratio -3441.109162 Model 3: discrete -3344.185046 Model 7: beta -3369.288535 Model 8: beta&w>1 -3343.969934 Model 0 vs 1 147.979292 Model 2 vs 1 45.44451200000003 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.983* 4.288 50 I 0.999** 4.344 52 T 0.999** 4.344 69 Q 0.530 2.773 84 Y 0.544 2.820 113 E 0.970* 4.246 115 C 0.966* 4.232 131 T 1.000** 4.345 133 E 0.897 4.001 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: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.980* 4.516 +- 0.959 50 I 0.999** 4.584 +- 0.829 52 T 0.999** 4.584 +- 0.828 113 E 0.950 4.378 +- 1.101 115 C 0.955* 4.416 +- 1.088 131 T 1.000** 4.586 +- 0.825 133 E 0.855 4.013 +- 1.437 Model 8 vs 7 50.63720199999989 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.988* 3.744 42 R 0.641 2.751 50 I 1.000** 3.778 52 T 1.000** 3.778 69 Q 0.662 2.806 84 Y 0.728 3.003 113 E 0.984* 3.733 115 C 0.979* 3.719 131 T 1.000** 3.778 133 E 0.941 3.610 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: S24_SFBB1) Pr(w>1) post mean +- SE for w 2 E 0.986* 3.942 +- 0.866 42 R 0.550 2.458 +- 1.513 50 I 0.999** 3.981 +- 0.796 52 T 1.000** 3.981 +- 0.795 69 Q 0.603 2.671 +- 1.572 84 Y 0.637 2.736 +- 1.497 113 E 0.975* 3.896 +- 0.910 115 C 0.974* 3.898 +- 0.923 131 T 1.000** 3.982 +- 0.795 133 E 0.917 3.700 +- 1.126