--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri May 25 03:02:23 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_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/DNG_A1/NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8578.98 -8625.61 2 -8576.99 -8635.01 -------------------------------------- TOTAL -8577.56 -8634.32 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/DNG_A1/NS1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 7.061918 0.217229 6.119356 7.933400 7.046622 588.49 600.44 1.000 r(A<->C){all} 0.031058 0.000031 0.020392 0.042085 0.030903 704.83 786.88 1.000 r(A<->G){all} 0.227081 0.000289 0.195949 0.260514 0.227040 606.11 660.73 1.000 r(A<->T){all} 0.056509 0.000052 0.043015 0.070569 0.056291 677.10 769.34 1.000 r(C<->G){all} 0.022135 0.000039 0.011028 0.034886 0.021683 709.93 734.92 1.001 r(C<->T){all} 0.635477 0.000411 0.596931 0.674172 0.635463 434.52 575.90 1.000 r(G<->T){all} 0.027740 0.000051 0.014001 0.041716 0.027284 746.40 746.72 1.000 pi(A){all} 0.347892 0.000109 0.327683 0.368054 0.347799 758.57 970.62 1.000 pi(C){all} 0.228362 0.000079 0.209986 0.244634 0.228234 765.18 794.12 1.000 pi(G){all} 0.226861 0.000088 0.209940 0.245728 0.226704 671.77 721.30 1.001 pi(T){all} 0.196886 0.000060 0.180936 0.211466 0.196766 898.71 957.78 1.000 alpha{1,2} 0.208197 0.000178 0.182822 0.233707 0.207404 1266.30 1279.09 1.000 alpha{3} 5.487497 1.109989 3.615456 7.584599 5.368261 1135.16 1318.08 1.000 pinvar{all} 0.139925 0.000532 0.095227 0.185246 0.139287 915.72 1112.14 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 -8230.639844 Model 2: PositiveSelection -8230.639844 Model 0: one-ratio -8359.991238 Model 3: discrete -8150.736716 Model 7: beta -8155.178613 Model 8: beta&w>1 -8151.584891 Model 0 vs 1 258.70278800000233 Model 2 vs 1 0.0 Model 8 vs 7 7.187443999999232 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis 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:FJ410223|Organism:Dengue_virus_2|Strain_Name:DENV-2/VN/BID-V1869/2007|Protein_Name:Nonstructural_protein_NS1|Gene_Symbol:NS1) Pr(w>1) post mean +- SE for w 94 K 0.679 1.227 +- 0.412 128 S 0.612 1.163 +- 0.438 131 Q 0.753 1.297 +- 0.369 178 F 0.561 1.112 +- 0.455