--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Apr 16 13:52:01 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= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AM/batch2/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/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -11370.18 -11414.43 2 -11370.19 -11414.59 -------------------------------------- TOTAL -11370.18 -11414.51 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AM/batch2/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/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 6.788471 0.094836 6.155887 7.368659 6.786524 676.34 821.55 1.000 r(A<->C){all} 0.107162 0.000070 0.091007 0.123545 0.106991 668.05 705.78 1.000 r(A<->G){all} 0.310907 0.000370 0.272288 0.347417 0.311561 319.83 408.85 1.000 r(A<->T){all} 0.093456 0.000072 0.077172 0.109695 0.093146 643.67 691.79 1.000 r(C<->G){all} 0.063819 0.000057 0.048840 0.078160 0.063342 729.08 757.80 1.000 r(C<->T){all} 0.329600 0.000420 0.291438 0.371954 0.328484 319.37 437.92 1.000 r(G<->T){all} 0.095055 0.000090 0.077447 0.114257 0.094688 723.23 753.85 1.003 pi(A){all} 0.353395 0.000149 0.330538 0.377653 0.353542 569.64 579.71 1.000 pi(C){all} 0.221142 0.000115 0.199015 0.241226 0.221232 588.32 613.62 1.001 pi(G){all} 0.241231 0.000118 0.220986 0.262965 0.241322 647.19 677.17 1.001 pi(T){all} 0.184232 0.000091 0.166427 0.203442 0.184077 588.54 626.01 1.000 alpha{1,2} 0.461161 0.001704 0.385411 0.542779 0.458314 1030.56 1175.59 1.000 alpha{3} 2.270255 0.118429 1.625646 2.950286 2.248987 1254.35 1307.79 1.000 pinvar{all} 0.068206 0.000523 0.025267 0.113319 0.066902 858.76 1048.13 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 -8780.802191 Model 2: PositiveSelection -8725.666742 Model 0: one-ratio -9263.633309 Model 3: discrete -8701.755116 Model 7: beta -8732.755948 Model 8: beta&w>1 -8686.864626 Model 0 vs 1 965.6622360000001 Model 2 vs 1 110.27089800000249 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: C.ZA.08.as03_0513.KM262928_) Pr(w>1) post mean +- SE for w 8 P 0.820 2.566 9 N 0.997** 2.904 107 V 1.000** 2.910 125 R 0.999** 2.908 131 C 0.997** 2.904 149 M 1.000** 2.910 155 S 1.000** 2.910 161 L 0.989* 2.889 165 K 1.000** 2.910 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: C.ZA.08.as03_0513.KM262928_) Pr(w>1) post mean +- SE for w 8 P 0.789 2.363 +- 0.798 9 N 0.996** 2.784 +- 0.469 107 V 1.000** 2.792 +- 0.455 125 R 0.998** 2.788 +- 0.460 131 C 0.995** 2.782 +- 0.470 149 M 1.000** 2.791 +- 0.455 155 S 1.000** 2.792 +- 0.455 161 L 0.975* 2.735 +- 0.521 165 K 1.000** 2.792 +- 0.455 Model 8 vs 7 91.78264399999898 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: C.ZA.08.as03_0513.KM262928_) Pr(w>1) post mean +- SE for w 8 P 0.849 2.147 9 N 0.995** 2.360 107 V 1.000** 2.367 125 R 0.998** 2.364 131 C 0.995** 2.360 149 M 1.000** 2.366 155 S 1.000** 2.367 161 L 0.981* 2.340 165 K 1.000** 2.367 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: C.ZA.08.as03_0513.KM262928_) Pr(w>1) post mean +- SE for w 8 P 0.777 2.148 +- 0.658 9 N 0.993** 2.488 +- 0.134 107 V 1.000** 2.500 +- 0.011 125 R 0.996** 2.494 +- 0.098 131 C 0.992** 2.488 +- 0.138 149 M 0.999** 2.499 +- 0.042 155 S 1.000** 2.500 +- 0.016 161 L 0.963* 2.442 +- 0.296 165 K 1.000** 2.500 +- 0.006