--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun May 27 10:19:27 WEST 2018 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=/opt/ADOPS1/DNG_A1/NS1_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_4/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/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -9005.40 -9052.54 2 -9008.00 -9052.33 -------------------------------------- TOTAL -9006.02 -9052.44 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_4/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/DNG_A1/NS1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 7.267033 0.207688 6.316381 8.123070 7.255604 474.90 678.07 1.001 r(A<->C){all} 0.033417 0.000028 0.022876 0.043695 0.033182 745.08 762.79 1.000 r(A<->G){all} 0.243976 0.000309 0.208940 0.276689 0.243568 452.23 539.12 1.001 r(A<->T){all} 0.049546 0.000040 0.037260 0.062083 0.049228 830.91 949.26 1.000 r(C<->G){all} 0.030012 0.000040 0.017701 0.042201 0.029716 884.89 922.87 1.000 r(C<->T){all} 0.619807 0.000426 0.577332 0.657649 0.620377 447.84 515.37 1.001 r(G<->T){all} 0.023242 0.000045 0.011289 0.036639 0.022779 797.58 912.72 1.000 pi(A){all} 0.350688 0.000110 0.330331 0.371544 0.350666 859.01 972.46 1.002 pi(C){all} 0.231045 0.000076 0.213549 0.247780 0.230827 818.35 872.63 1.000 pi(G){all} 0.220174 0.000081 0.202036 0.237744 0.220215 513.91 535.67 1.001 pi(T){all} 0.198093 0.000064 0.182949 0.214077 0.197810 634.96 648.82 1.004 alpha{1,2} 0.212089 0.000187 0.185677 0.239768 0.211622 1320.14 1385.15 1.000 alpha{3} 5.056736 0.873651 3.383337 6.890033 4.948809 1242.73 1335.18 1.000 pinvar{all} 0.136396 0.000505 0.093612 0.180194 0.135518 1385.59 1433.08 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 -8637.396459 Model 2: PositiveSelection -8637.396459 Model 0: one-ratio -8760.474374 Model 3: discrete -8543.545578 Model 7: beta -8549.940326 Model 8: beta&w>1 -8546.864166 Model 0 vs 1 246.1558299999997 Model 2 vs 1 0.0 Model 8 vs 7 6.152320000001055 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: gb:GQ398258|Organism:Dengue_virus_2|Strain_Name:DENV-2/ID/1016DN/1975|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1) Pr(w>1) post mean +- SE for w 94 K 0.670 0.752 98 Q 0.687 0.764 128 L 0.978* 0.983 131 Q 0.899 0.924 178 F 0.970* 0.978 224 H 0.579 0.683 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: gb:GQ398258|Organism:Dengue_virus_2|Strain_Name:DENV-2/ID/1016DN/1975|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1) Pr(w>1) post mean +- SE for w 128 L 0.717 1.267 +- 0.392 178 F 0.772 1.316 +- 0.374