--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Mar 15 21:22:40 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_2/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -49253.20 -49295.51 2 -49251.92 -49291.59 -------------------------------------- TOTAL -49252.37 -49294.83 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 8.520280 0.070648 8.006031 9.029888 8.512646 880.50 906.37 1.000 r(A<->C){all} 0.132237 0.000027 0.121210 0.141730 0.132403 346.67 409.01 1.000 r(A<->G){all} 0.299126 0.000140 0.276629 0.321858 0.299409 172.85 225.56 1.001 r(A<->T){all} 0.056602 0.000011 0.050060 0.062777 0.056502 601.82 674.36 1.000 r(C<->G){all} 0.067927 0.000023 0.058703 0.077256 0.067770 517.03 613.55 1.003 r(C<->T){all} 0.346730 0.000156 0.323732 0.371366 0.346299 206.96 215.76 1.001 r(G<->T){all} 0.097379 0.000026 0.087467 0.106972 0.097266 366.65 396.22 1.004 pi(A){all} 0.397327 0.000049 0.383806 0.410914 0.397330 410.80 426.42 1.000 pi(C){all} 0.175425 0.000028 0.164550 0.184760 0.175509 266.64 299.75 1.000 pi(G){all} 0.220099 0.000034 0.208299 0.231055 0.219879 180.26 296.49 1.000 pi(T){all} 0.207149 0.000035 0.194870 0.218344 0.207041 361.43 385.63 1.000 alpha{1,2} 0.483374 0.000519 0.442819 0.528907 0.482658 1051.31 1087.49 1.000 alpha{3} 1.056696 0.004022 0.925692 1.174112 1.056890 985.27 1052.47 1.000 pinvar{all} 0.187538 0.000204 0.160950 0.216355 0.187694 1031.23 1058.84 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 -40805.901807 Model 2: PositiveSelection -40168.634087 Model 0: one-ratio -43375.868154 Model 3: discrete -40136.944168 Model 7: beta -40606.662897 Model 8: beta&w>1 -40033.544763 Model 0 vs 1 5139.932694000003 Model 2 vs 1 1274.535440000007 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.TH.06.98PB2.EU743784_) Pr(w>1) post mean +- SE for w 10 W 1.000** 3.483 15 T 0.990** 3.459 73 Y 1.000** 3.483 119 P 1.000** 3.483 120 T 1.000** 3.482 121 T 1.000** 3.483 122 S 1.000** 3.483 139 K 0.871 3.162 140 Q 1.000** 3.483 143 Y 0.987* 3.451 155 N 0.995** 3.471 156 K 1.000** 3.483 157 T 1.000** 3.483 158 T 1.000** 3.483 168 V 0.998** 3.479 177 S 0.541 2.344 200 N 0.546 2.357 208 N 0.992** 3.462 249 T 0.956* 3.373 259 S 0.575 2.429 261 Q 1.000** 3.483 268 S 0.999** 3.480 276 H 1.000** 3.483 286 D 1.000** 3.483 299 G 0.992** 3.463 300 T 1.000** 3.483 303 E 0.998** 3.479 306 K 1.000** 3.483 307 Q 1.000** 3.483 309 A 1.000** 3.483 310 K 1.000** 3.483 313 K 1.000** 3.483 315 H 0.780 2.938 319 V 1.000** 3.483 323 S 0.999** 3.481 347 S 0.575 2.428 348 Q 1.000** 3.483 352 A 0.962* 3.388 354 T 1.000** 3.483 355 I 1.000** 3.483 357 S 1.000** 3.483 358 T 0.970* 3.408 385 S 1.000** 3.483 387 V 1.000** 3.483 391 L 1.000** 3.483 405 N 1.000** 3.483 406 T 1.000** 3.483 407 A 1.000** 3.483 456 I 0.779 2.934 548 A 1.000** 3.483 553 S 0.999** 3.481 560 Y 1.000** 3.483 561 D 1.000** 3.483 562 T 1.000** 3.483 570 K 0.556 2.379 576 S 0.691 2.717 580 D 1.000** 3.483 581 L 1.000** 3.483 584 G 1.000** 3.483 614 D 0.998** 3.479 661 T 1.000** 3.483 663 H 0.988* 3.453 664 Q 0.903 3.242 686 V 1.000** 3.483 690 S 0.999** 3.481 696 A 1.000** 3.482 710 R 1.000** 3.483 726 G 1.000** 3.483 730 L 0.789 2.958 735 L 0.999** 3.481 749 L 0.546 2.356 770 A 1.000** 3.483 771 W 1.000** 3.483 775 L 0.998** 3.478 776 H 0.694 2.724 785 L 0.990* 3.458 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: 01_AE.TH.06.98PB2.EU743784_) Pr(w>1) post mean +- SE for w 10 W 1.000** 3.500 +- 0.012 15 T 0.989* 3.473 +- 0.261 73 Y 1.000** 3.500 +- 0.000 119 P 1.000** 3.500 +- 0.000 120 T 1.000** 3.500 +- 0.035 121 T 1.000** 3.500 +- 0.000 122 S 1.000** 3.500 +- 0.000 139 K 0.851 3.129 +- 0.889 140 Q 1.000** 3.500 +- 0.017 143 Y 0.985* 3.462 +- 0.304 155 N 0.994** 3.486 +- 0.189 156 K 1.000** 3.500 +- 0.003 157 T 1.000** 3.500 +- 0.000 158 T 1.000** 3.500 +- 0.001 168 V 0.998** 3.495 +- 0.106 177 S 0.513 2.283 +- 1.250 200 N 0.513 2.281 +- 1.250 208 N 0.990** 3.476 +- 0.246 249 T 0.949 3.372 +- 0.551 259 S 0.544 2.360 +- 1.245 261 Q 1.000** 3.500 +- 0.000 268 S 0.999** 3.496 +- 0.094 276 H 1.000** 3.500 +- 0.009 286 D 1.000** 3.500 +- 0.002 299 G 0.990** 3.476 +- 0.243 300 T 1.000** 3.500 +- 0.009 303 E 0.998** 3.495 +- 0.107 306 K 1.000** 3.500 +- 0.018 307 Q 1.000** 3.500 +- 0.000 309 A 1.000** 3.500 +- 0.017 310 K 1.000** 3.500 +- 0.000 313 K 1.000** 3.500 +- 0.007 315 H 0.755 2.888 +- 1.075 319 V 1.000** 3.500 +- 0.000 323 S 0.999** 3.498 +- 0.063 347 S 0.544 2.361 +- 1.245 348 Q 1.000** 3.500 +- 0.000 352 A 0.956* 3.389 +- 0.515 354 T 1.000** 3.500 +- 0.000 355 I 1.000** 3.500 +- 0.000 357 S 1.000** 3.500 +- 0.000 358 T 0.965* 3.412 +- 0.460 385 S 1.000** 3.500 +- 0.000 387 V 1.000** 3.500 +- 0.000 391 L 1.000** 3.500 +- 0.012 405 N 1.000** 3.500 +- 0.000 406 T 1.000** 3.500 +- 0.000 407 A 1.000** 3.500 +- 0.000 456 I 0.754 2.885 +- 1.076 548 A 1.000** 3.500 +- 0.024 553 S 0.999** 3.498 +- 0.067 560 Y 1.000** 3.500 +- 0.000 561 D 1.000** 3.500 +- 0.001 562 T 1.000** 3.500 +- 0.011 570 K 0.525 2.313 +- 1.248 576 S 0.658 2.645 +- 1.186 580 D 1.000** 3.500 +- 0.000 581 L 1.000** 3.500 +- 0.033 584 G 1.000** 3.500 +- 0.000 614 D 0.998** 3.496 +- 0.106 661 T 1.000** 3.500 +- 0.026 663 H 0.986* 3.465 +- 0.293 664 Q 0.890 3.226 +- 0.781 686 V 1.000** 3.500 +- 0.014 690 S 0.999** 3.498 +- 0.067 696 A 1.000** 3.499 +- 0.039 710 R 1.000** 3.500 +- 0.005 726 G 1.000** 3.500 +- 0.001 730 L 0.767 2.918 +- 1.056 735 L 0.999** 3.498 +- 0.077 749 L 0.515 2.288 +- 1.249 770 A 1.000** 3.500 +- 0.006 771 W 1.000** 3.500 +- 0.007 775 L 0.998** 3.494 +- 0.124 776 H 0.665 2.661 +- 1.180 785 L 0.988* 3.471 +- 0.269 Model 8 vs 7 1146.2362680000078 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.TH.06.98PB2.EU743784_) Pr(w>1) post mean +- SE for w 10 W 1.000** 3.021 15 T 0.990** 3.001 73 Y 1.000** 3.021 119 P 1.000** 3.021 120 T 1.000** 3.021 121 T 1.000** 3.021 122 S 1.000** 3.021 139 K 0.879 2.772 140 Q 1.000** 3.021 143 Y 0.987* 2.995 155 N 0.994** 3.009 156 K 1.000** 3.021 157 T 1.000** 3.021 158 T 1.000** 3.021 168 V 0.998** 3.018 177 S 0.647 2.280 200 N 0.597 2.185 208 N 0.991** 3.002 249 T 0.966* 2.950 259 S 0.669 2.332 261 Q 1.000** 3.021 268 S 0.998** 3.018 276 H 1.000** 3.021 286 D 1.000** 3.021 299 G 0.990** 3.001 300 T 1.000** 3.021 303 E 0.998** 3.017 306 K 1.000** 3.021 307 Q 1.000** 3.021 309 A 1.000** 3.021 310 K 1.000** 3.021 313 K 1.000** 3.021 315 H 0.806 2.618 319 V 1.000** 3.021 323 S 0.999** 3.020 347 S 0.689 2.371 348 Q 1.000** 3.021 352 A 0.956* 2.930 354 T 1.000** 3.021 355 I 1.000** 3.021 357 S 1.000** 3.021 358 T 0.972* 2.963 385 S 1.000** 3.021 387 V 1.000** 3.021 391 L 1.000** 3.021 405 N 1.000** 3.021 406 T 1.000** 3.021 407 A 1.000** 3.021 442 R 0.503 1.988 456 I 0.800 2.607 548 A 1.000** 3.021 553 S 0.999** 3.020 560 Y 1.000** 3.021 561 D 1.000** 3.021 562 T 1.000** 3.021 570 K 0.623 2.234 576 S 0.730 2.462 580 D 1.000** 3.021 581 L 1.000** 3.021 584 G 1.000** 3.021 614 D 0.998** 3.017 661 T 1.000** 3.021 663 H 0.989* 2.999 664 Q 0.926 2.866 686 V 1.000** 3.021 690 S 0.999** 3.019 696 A 1.000** 3.021 710 R 1.000** 3.021 726 G 1.000** 3.021 730 L 0.811 2.623 735 L 0.999** 3.019 749 L 0.628 2.246 770 A 1.000** 3.021 771 W 1.000** 3.021 775 L 0.998** 3.016 776 H 0.740 2.479 785 L 0.989* 2.999 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: 01_AE.TH.06.98PB2.EU743784_) Pr(w>1) post mean +- SE for w 4 K 0.643 1.934 +- 0.761 10 W 1.000** 2.506 +- 0.079 15 T 0.998** 2.502 +- 0.108 73 Y 1.000** 2.506 +- 0.079 119 P 1.000** 2.506 +- 0.079 120 T 1.000** 2.506 +- 0.080 121 T 1.000** 2.506 +- 0.079 122 S 1.000** 2.506 +- 0.079 134 E 0.934 2.397 +- 0.391 139 K 0.985* 2.480 +- 0.197 140 Q 1.000** 2.506 +- 0.079 143 Y 0.997** 2.502 +- 0.111 153 P 0.904 2.349 +- 0.467 155 N 0.999** 2.505 +- 0.091 156 K 1.000** 2.506 +- 0.079 157 T 1.000** 2.506 +- 0.079 158 T 1.000** 2.506 +- 0.079 168 V 1.000** 2.505 +- 0.086 177 S 0.906 2.351 +- 0.471 200 N 0.947 2.417 +- 0.356 208 N 0.998** 2.504 +- 0.098 247 G 0.813 2.203 +- 0.620 249 T 0.994** 2.495 +- 0.144 251 T 0.529 1.747 +- 0.800 259 S 0.939 2.404 +- 0.383 261 Q 1.000** 2.506 +- 0.079 268 S 1.000** 2.506 +- 0.084 276 H 1.000** 2.506 +- 0.079 286 D 1.000** 2.506 +- 0.079 292 R 0.523 1.739 +- 0.798 294 Y 0.730 2.071 +- 0.707 299 G 0.999** 2.504 +- 0.097 300 T 1.000** 2.506 +- 0.079 302 N 0.873 2.301 +- 0.524 303 E 1.000** 2.506 +- 0.084 306 K 1.000** 2.506 +- 0.079 307 Q 1.000** 2.506 +- 0.079 309 A 1.000** 2.506 +- 0.079 310 K 1.000** 2.506 +- 0.079 313 K 1.000** 2.506 +- 0.079 315 H 0.965* 2.447 +- 0.296 319 V 1.000** 2.506 +- 0.079 323 S 1.000** 2.506 +- 0.084 347 S 0.939 2.405 +- 0.382 348 Q 1.000** 2.506 +- 0.079 352 A 0.993** 2.494 +- 0.144 354 T 1.000** 2.506 +- 0.079 355 I 1.000** 2.506 +- 0.079 357 S 1.000** 2.506 +- 0.079 358 T 0.995** 2.498 +- 0.132 374 G 0.858 2.276 +- 0.551 385 S 1.000** 2.506 +- 0.079 387 V 1.000** 2.506 +- 0.079 389 N 0.711 2.041 +- 0.722 391 L 1.000** 2.506 +- 0.079 405 N 1.000** 2.506 +- 0.079 406 T 1.000** 2.506 +- 0.079 407 A 1.000** 2.506 +- 0.079 409 T 0.776 2.145 +- 0.663 442 R 0.921 2.376 +- 0.427 456 I 0.965* 2.447 +- 0.296 459 M 0.881 2.312 +- 0.514 476 I 0.794 2.175 +- 0.639 548 A 1.000** 2.506 +- 0.079 553 S 1.000** 2.506 +- 0.082 560 Y 1.000** 2.506 +- 0.079 561 D 1.000** 2.506 +- 0.079 562 T 1.000** 2.506 +- 0.079 570 K 0.924 2.381 +- 0.422 576 S 0.970* 2.453 +- 0.272 580 D 1.000** 2.506 +- 0.079 581 L 1.000** 2.506 +- 0.080 584 G 1.000** 2.506 +- 0.079 586 L 0.533 1.751 +- 0.804 614 D 1.000** 2.506 +- 0.084 617 N 0.587 1.847 +- 0.780 661 T 1.000** 2.506 +- 0.080 663 H 0.998** 2.502 +- 0.109 664 Q 0.981* 2.475 +- 0.227 686 V 1.000** 2.506 +- 0.079 690 S 1.000** 2.506 +- 0.082 696 A 1.000** 2.506 +- 0.080 710 R 1.000** 2.506 +- 0.079 726 G 1.000** 2.506 +- 0.079 730 L 0.939 2.404 +- 0.392 735 L 1.000** 2.505 +- 0.086 739 Q 0.678 1.979 +- 0.759 749 L 0.930 2.390 +- 0.408 767 T 0.739 2.088 +- 0.695 770 A 1.000** 2.506 +- 0.079 771 W 1.000** 2.506 +- 0.079 775 L 0.999** 2.505 +- 0.092 776 H 0.953* 2.428 +- 0.337 785 L 0.997** 2.502 +- 0.112