--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Mar 18 10:16:48 WET 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=/usr/bin/ input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/HIV1_A1/GAG_1_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_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/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -17747.97 -17798.50 2 -17751.04 -17799.62 -------------------------------------- TOTAL -17748.62 -17799.21 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_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/ADOPS/HIV1_A1/GAG_1_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} 3.738079 0.018388 3.479724 4.012158 3.737135 888.42 1045.81 1.003 r(A<->C){all} 0.089414 0.000031 0.078181 0.099606 0.089356 669.68 683.54 1.009 r(A<->G){all} 0.287495 0.000221 0.258821 0.316194 0.287047 453.38 476.43 1.004 r(A<->T){all} 0.047975 0.000019 0.039622 0.056101 0.047870 771.16 797.17 1.004 r(C<->G){all} 0.045823 0.000027 0.035820 0.055943 0.045774 706.61 738.61 1.006 r(C<->T){all} 0.469394 0.000317 0.436139 0.505615 0.469824 397.23 440.44 1.010 r(G<->T){all} 0.059898 0.000038 0.047500 0.071745 0.059791 563.99 606.61 1.062 pi(A){all} 0.401985 0.000090 0.384236 0.421298 0.401816 486.78 628.14 1.002 pi(C){all} 0.199067 0.000060 0.183174 0.213420 0.199110 493.84 601.82 1.048 pi(G){all} 0.220966 0.000057 0.205744 0.234911 0.220934 633.51 647.89 1.006 pi(T){all} 0.177982 0.000060 0.163154 0.193371 0.177810 635.65 676.37 1.041 alpha{1,2} 0.340883 0.000561 0.291903 0.384577 0.339862 1113.27 1180.76 1.002 alpha{3} 2.151079 0.074632 1.644252 2.690945 2.131353 1344.51 1345.19 1.002 pinvar{all} 0.205728 0.000535 0.160916 0.250257 0.205579 1025.00 1149.94 1.003 ------------------------------------------------------------------------------------------------------ * 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 -16266.313708 Model 2: PositiveSelection -16178.783957 Model 0: one-ratio -17191.380326 Model 3: discrete -16121.113931 Model 7: beta -16191.48603 Model 8: beta&w>1 -16101.849381 Model 0 vs 1 1850.1332359999979 Model 2 vs 1 175.05950200000007 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: CD.NP.11.11NP079.KU341727_) Pr(w>1) post mean +- SE for w 13 K 0.990** 2.788 26 H 0.999** 2.803 52 S 0.974* 2.759 65 A 0.997** 2.800 77 H 0.985* 2.779 88 A 0.989* 2.786 89 G 1.000** 2.806 91 E 0.733 2.324 113 K 0.785 2.418 114 G 0.778 2.406 126 L 0.700 2.264 134 A 0.988* 2.784 202 L 0.955* 2.726 210 I 1.000** 2.806 239 G 0.998** 2.803 267 V 1.000** 2.806 344 G 0.712 2.286 359 S 1.000** 2.806 360 T 0.999** 2.805 371 S 0.994** 2.796 424 N 0.894 2.615 450 P 1.000** 2.806 457 T 1.000** 2.806 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: CD.NP.11.11NP079.KU341727_) Pr(w>1) post mean +- SE for w 13 K 0.987* 2.550 +- 0.312 26 H 0.998** 2.570 +- 0.271 52 S 0.966* 2.515 +- 0.379 65 A 0.995** 2.565 +- 0.285 77 H 0.976* 2.536 +- 0.351 82 T 0.510 1.774 +- 0.766 88 A 0.985* 2.547 +- 0.318 89 G 1.000** 2.573 +- 0.261 91 E 0.742 2.130 +- 0.678 113 K 0.792 2.207 +- 0.633 114 G 0.778 2.187 +- 0.650 126 L 0.676 2.041 +- 0.738 134 A 0.980* 2.543 +- 0.338 202 L 0.938 2.473 +- 0.451 210 I 1.000** 2.573 +- 0.263 239 G 0.998** 2.570 +- 0.272 267 V 0.999** 2.573 +- 0.264 344 G 0.706 2.079 +- 0.711 359 S 1.000** 2.573 +- 0.262 360 T 0.999** 2.572 +- 0.266 366 S 0.515 1.780 +- 0.762 371 S 0.991** 2.559 +- 0.300 424 N 0.871 2.355 +- 0.563 450 P 1.000** 2.573 +- 0.261 457 T 1.000** 2.573 +- 0.261 Model 8 vs 7 179.27329800000007 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: CD.NP.11.11NP079.KU341727_) Pr(w>1) post mean +- SE for w 13 K 0.999** 2.235 18 R 0.507 1.519 26 H 1.000** 2.237 52 S 0.995** 2.231 65 A 0.999** 2.236 77 H 0.996** 2.232 82 T 0.831 1.993 88 A 0.998** 2.234 89 G 1.000** 2.237 91 E 0.945 2.158 113 K 0.961* 2.182 114 G 0.955* 2.173 126 L 0.896 2.088 134 A 0.997** 2.233 202 L 0.988* 2.220 210 I 1.000** 2.237 239 G 1.000** 2.237 267 V 1.000** 2.237 344 G 0.927 2.132 359 S 1.000** 2.237 360 T 1.000** 2.237 366 S 0.835 2.000 371 S 0.998** 2.235 424 N 0.972* 2.197 450 P 1.000** 2.237 457 T 1.000** 2.237 468 L 0.589 1.633 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: CD.NP.11.11NP079.KU341727_) Pr(w>1) post mean +- SE for w 13 K 0.986* 2.478 +- 0.184 26 H 0.998** 2.497 +- 0.073 52 S 0.975* 2.461 +- 0.246 65 A 0.997** 2.496 +- 0.079 77 H 0.987* 2.480 +- 0.178 82 T 0.563 1.803 +- 0.793 88 A 0.984* 2.475 +- 0.197 89 G 1.000** 2.500 +- 0.003 91 E 0.728 2.071 +- 0.702 113 K 0.757 2.118 +- 0.675 114 G 0.772 2.141 +- 0.662 126 L 0.720 2.053 +- 0.717 134 A 0.991** 2.485 +- 0.152 202 L 0.959* 2.435 +- 0.313 210 I 1.000** 2.500 +- 0.021 239 G 0.998** 2.497 +- 0.069 267 V 1.000** 2.500 +- 0.025 344 G 0.737 2.083 +- 0.699 359 S 1.000** 2.500 +- 0.025 360 T 0.999** 2.499 +- 0.043 366 S 0.534 1.759 +- 0.795 371 S 0.993** 2.490 +- 0.128 424 N 0.889 2.325 +- 0.497 450 P 1.000** 2.500 +- 0.001 457 T 1.000** 2.500 +- 0.007