--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Mar 18 03:59:30 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/ENV_1_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_5/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/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -48140.15 -48190.84 2 -48143.73 -48181.76 -------------------------------------- TOTAL -48140.82 -48190.14 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_5/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/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 7.924580 0.038989 7.531423 8.295759 7.921610 997.89 1115.63 1.000 r(A<->C){all} 0.137237 0.000026 0.127058 0.146250 0.137221 494.31 571.21 1.003 r(A<->G){all} 0.291069 0.000096 0.272852 0.310744 0.290791 208.45 262.94 1.008 r(A<->T){all} 0.058761 0.000009 0.052875 0.064499 0.058707 487.19 582.07 1.000 r(C<->G){all} 0.075342 0.000023 0.066137 0.084448 0.075257 465.61 488.87 1.000 r(C<->T){all} 0.346549 0.000111 0.325588 0.365750 0.346818 205.62 250.05 1.014 r(G<->T){all} 0.091042 0.000019 0.082465 0.099355 0.091067 640.52 641.94 1.000 pi(A){all} 0.389313 0.000041 0.377038 0.402714 0.389421 186.84 288.88 1.007 pi(C){all} 0.175724 0.000022 0.166923 0.185081 0.175724 295.69 404.61 1.002 pi(G){all} 0.216852 0.000026 0.206623 0.226496 0.216820 364.09 377.65 1.002 pi(T){all} 0.218110 0.000031 0.207745 0.229529 0.218010 462.31 482.06 1.009 alpha{1,2} 0.447391 0.000379 0.408282 0.483509 0.446617 1170.88 1257.11 1.000 alpha{3} 1.030798 0.004949 0.902775 1.171946 1.028718 1217.04 1259.96 1.000 pinvar{all} 0.143854 0.000182 0.116537 0.168512 0.144010 949.51 1031.44 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 -39389.370011 Model 2: PositiveSelection -38756.699399 Model 0: one-ratio -41701.418989 Model 3: discrete -38738.678452 Model 7: beta -39270.501835 Model 8: beta&w>1 -38676.877865 Model 0 vs 1 4624.097955999998 Model 2 vs 1 1265.3412240000034 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: B.GB.08.D650_E9.HQ595775_) Pr(w>1) post mean +- SE for w 7 R 1.000** 3.625 10 H 0.993** 3.609 14 T 0.525 2.377 77 E 1.000** 3.626 126 N 1.000** 3.626 127 S 1.000** 3.626 128 S 1.000** 3.626 129 E 1.000** 3.626 130 E 1.000** 3.626 131 R 1.000** 3.626 132 G 1.000** 3.626 149 Q 0.999** 3.624 152 Y 0.911 3.393 164 D 1.000** 3.626 165 N 1.000** 3.626 166 T 1.000** 3.625 167 T 1.000** 3.626 177 V 0.822 3.160 184 S 0.999** 3.625 215 T 0.973* 3.554 252 L 0.987* 3.593 254 D 0.834 3.189 256 T 0.945 3.481 268 E 1.000** 3.626 275 N 1.000** 3.626 283 H 1.000** 3.626 294 E 1.000** 3.626 302 E 1.000** 3.626 305 Y 1.000** 3.626 306 Q 1.000** 3.626 308 V 1.000** 3.626 309 E 1.000** 3.626 314 Q 0.996** 3.616 319 V 1.000** 3.626 321 D 1.000** 3.626 322 Q 0.997** 3.618 323 S 1.000** 3.626 348 Q 1.000** 3.626 378 S 1.000** 3.626 380 P 1.000** 3.626 384 T 1.000** 3.626 398 N 1.000** 3.626 399 N 1.000** 3.626 400 D 1.000** 3.626 401 T 1.000** 3.626 436 R 1.000** 3.626 542 A 0.998** 3.620 547 N 1.000** 3.626 554 L 1.000** 3.626 555 E 1.000** 3.626 556 Y 1.000** 3.626 564 Q 0.984* 3.584 570 D 0.980* 3.573 574 N 1.000** 3.626 575 L 0.984* 3.583 578 T 1.000** 3.626 608 D 0.998** 3.620 654 H 0.514 2.349 655 H 1.000** 3.626 657 A 0.976* 3.564 658 P 0.700 2.839 680 G 0.999** 3.625 720 A 0.998** 3.620 760 I 0.995** 3.614 761 V 0.989* 3.596 764 T 1.000** 3.626 765 Y 1.000** 3.626 769 L 0.998** 3.621 779 L 0.840 3.206 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: B.GB.08.D650_E9.HQ595775_) Pr(w>1) post mean +- SE for w 7 R 1.000** 3.499 +- 0.054 10 H 0.994** 3.484 +- 0.198 14 T 0.564 2.409 +- 1.240 77 E 1.000** 3.500 +- 0.000 125 D 0.507 2.268 +- 1.250 126 N 1.000** 3.500 +- 0.000 127 S 1.000** 3.500 +- 0.000 128 S 1.000** 3.500 +- 0.000 129 E 1.000** 3.500 +- 0.000 130 E 1.000** 3.500 +- 0.000 131 R 1.000** 3.500 +- 0.000 132 G 1.000** 3.500 +- 0.000 149 Q 0.999** 3.498 +- 0.062 152 Y 0.920 3.301 +- 0.677 164 D 1.000** 3.500 +- 0.000 165 N 1.000** 3.500 +- 0.000 166 T 1.000** 3.499 +- 0.037 167 T 1.000** 3.500 +- 0.000 177 V 0.836 3.089 +- 0.926 184 S 0.999** 3.498 +- 0.062 215 T 0.976* 3.441 +- 0.379 252 L 0.987* 3.466 +- 0.288 254 D 0.859 3.148 +- 0.870 256 T 0.949 3.373 +- 0.549 268 E 1.000** 3.500 +- 0.002 275 N 1.000** 3.500 +- 0.011 283 H 1.000** 3.500 +- 0.018 294 E 1.000** 3.500 +- 0.002 302 E 1.000** 3.500 +- 0.025 305 Y 1.000** 3.500 +- 0.030 306 Q 1.000** 3.500 +- 0.000 308 V 1.000** 3.500 +- 0.001 309 E 1.000** 3.500 +- 0.002 314 Q 0.996** 3.490 +- 0.156 319 V 1.000** 3.500 +- 0.001 321 D 1.000** 3.500 +- 0.003 322 Q 0.997** 3.493 +- 0.132 323 S 1.000** 3.500 +- 0.003 348 Q 1.000** 3.500 +- 0.000 378 S 1.000** 3.500 +- 0.002 380 P 1.000** 3.500 +- 0.001 384 T 1.000** 3.500 +- 0.003 398 N 1.000** 3.500 +- 0.000 399 N 1.000** 3.500 +- 0.000 400 D 1.000** 3.500 +- 0.000 401 T 1.000** 3.500 +- 0.002 436 R 1.000** 3.500 +- 0.024 542 A 0.998** 3.495 +- 0.117 547 N 1.000** 3.500 +- 0.001 554 L 1.000** 3.500 +- 0.000 555 E 1.000** 3.500 +- 0.000 556 Y 1.000** 3.500 +- 0.002 564 Q 0.985* 3.462 +- 0.308 570 D 0.983* 3.457 +- 0.325 574 N 1.000** 3.500 +- 0.000 575 L 0.985* 3.462 +- 0.305 578 T 1.000** 3.500 +- 0.000 608 D 0.998** 3.495 +- 0.117 654 H 0.547 2.366 +- 1.245 655 H 1.000** 3.500 +- 0.004 657 A 0.978* 3.445 +- 0.365 658 P 0.712 2.779 +- 1.132 680 G 0.999** 3.499 +- 0.058 684 N 0.549 2.371 +- 1.244 720 A 0.998** 3.494 +- 0.124 760 I 0.996** 3.490 +- 0.161 761 V 0.990* 3.475 +- 0.250 764 T 1.000** 3.500 +- 0.013 765 Y 1.000** 3.500 +- 0.001 769 L 0.998** 3.495 +- 0.115 779 L 0.853 3.133 +- 0.885 Model 8 vs 7 1187.247940000001 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: B.GB.08.D650_E9.HQ595775_) Pr(w>1) post mean +- SE for w 7 R 1.000** 3.155 10 H 0.995** 3.145 14 T 0.667 2.414 77 E 1.000** 3.156 125 D 0.528 2.109 126 N 1.000** 3.156 127 S 1.000** 3.156 128 S 1.000** 3.156 129 E 1.000** 3.156 130 E 1.000** 3.156 131 R 1.000** 3.156 132 G 1.000** 3.156 149 Q 1.000** 3.155 152 Y 0.942 3.026 164 D 1.000** 3.156 165 N 1.000** 3.156 166 T 1.000** 3.156 167 T 1.000** 3.156 177 V 0.894 2.921 184 S 1.000** 3.155 215 T 0.977* 3.105 252 L 0.990** 3.134 254 D 0.877 2.884 256 T 0.966* 3.081 268 E 1.000** 3.156 275 N 1.000** 3.156 283 H 1.000** 3.156 294 E 1.000** 3.156 302 E 1.000** 3.156 305 Y 1.000** 3.156 306 Q 1.000** 3.156 308 V 1.000** 3.156 309 E 1.000** 3.156 314 Q 0.997** 3.149 319 V 1.000** 3.156 321 D 1.000** 3.156 322 Q 0.998** 3.151 323 S 1.000** 3.156 348 Q 1.000** 3.156 378 S 1.000** 3.156 380 P 1.000** 3.156 384 T 1.000** 3.156 398 N 1.000** 3.156 399 N 1.000** 3.156 400 D 1.000** 3.156 401 T 1.000** 3.156 436 R 1.000** 3.156 542 A 0.998** 3.152 547 N 1.000** 3.156 554 L 1.000** 3.156 555 E 1.000** 3.156 556 Y 1.000** 3.156 564 Q 0.988* 3.130 570 D 0.985* 3.122 574 N 1.000** 3.156 575 L 0.988* 3.129 578 T 1.000** 3.156 608 D 0.998** 3.152 654 H 0.656 2.385 655 H 1.000** 3.156 657 A 0.983* 3.119 658 P 0.791 2.688 680 G 0.999** 3.155 684 N 0.613 2.295 720 A 0.998** 3.153 760 I 0.996** 3.148 761 V 0.991** 3.136 764 T 1.000** 3.156 765 Y 1.000** 3.156 769 L 0.999** 3.153 779 L 0.885 2.900 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: B.GB.08.D650_E9.HQ595775_) Pr(w>1) post mean +- SE for w 7 R 0.999** 3.498 +- 0.079 10 H 0.981* 3.451 +- 0.352 77 E 1.000** 3.500 +- 0.000 126 N 1.000** 3.500 +- 0.001 127 S 1.000** 3.500 +- 0.000 128 S 1.000** 3.500 +- 0.000 129 E 1.000** 3.500 +- 0.000 130 E 1.000** 3.500 +- 0.000 131 R 1.000** 3.500 +- 0.000 132 G 1.000** 3.500 +- 0.000 149 Q 0.999** 3.497 +- 0.087 152 Y 0.772 2.913 +- 1.080 164 D 1.000** 3.500 +- 0.001 165 N 1.000** 3.500 +- 0.000 166 T 0.999** 3.498 +- 0.074 167 T 1.000** 3.500 +- 0.000 177 V 0.664 2.634 +- 1.219 184 S 0.999** 3.498 +- 0.078 215 T 0.889 3.215 +- 0.806 252 L 0.974* 3.433 +- 0.411 254 D 0.544 2.326 +- 1.281 256 T 0.870 3.166 +- 0.865 268 E 1.000** 3.500 +- 0.004 275 N 1.000** 3.500 +- 0.017 283 H 1.000** 3.500 +- 0.032 294 E 1.000** 3.500 +- 0.003 302 E 1.000** 3.499 +- 0.049 305 Y 0.999** 3.499 +- 0.059 306 Q 1.000** 3.500 +- 0.000 308 V 1.000** 3.500 +- 0.001 309 E 1.000** 3.500 +- 0.003 314 Q 0.989* 3.472 +- 0.269 319 V 1.000** 3.500 +- 0.001 321 D 1.000** 3.500 +- 0.005 322 Q 0.991** 3.477 +- 0.244 323 S 1.000** 3.500 +- 0.003 348 Q 1.000** 3.500 +- 0.000 378 S 1.000** 3.500 +- 0.004 380 P 1.000** 3.500 +- 0.001 384 T 1.000** 3.500 +- 0.004 398 N 1.000** 3.500 +- 0.000 399 N 1.000** 3.500 +- 0.001 400 D 1.000** 3.500 +- 0.000 401 T 1.000** 3.500 +- 0.004 436 R 1.000** 3.499 +- 0.038 542 A 0.993** 3.483 +- 0.208 547 N 1.000** 3.500 +- 0.001 554 L 1.000** 3.500 +- 0.000 555 E 1.000** 3.500 +- 0.000 556 Y 1.000** 3.500 +- 0.003 564 Q 0.958* 3.391 +- 0.518 570 D 0.920 3.295 +- 0.695 574 N 1.000** 3.500 +- 0.000 575 L 0.951* 3.375 +- 0.553 578 T 1.000** 3.500 +- 0.000 608 D 0.991** 3.477 +- 0.241 655 H 1.000** 3.500 +- 0.005 657 A 0.932 3.326 +- 0.646 680 G 0.998** 3.496 +- 0.107 720 A 0.995** 3.488 +- 0.175 760 I 0.984* 3.459 +- 0.321 761 V 0.960* 3.398 +- 0.502 764 T 1.000** 3.500 +- 0.021 765 Y 1.000** 3.500 +- 0.001 769 L 0.997** 3.491 +- 0.149 779 L 0.630 2.546 +- 1.246