--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Mar 15 01:46:38 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_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -48664.19 -48704.11 2 -48660.41 -48702.51 -------------------------------------- TOTAL -48661.08 -48703.60 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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/ENV_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} 7.870206 0.052154 7.441097 8.321572 7.870053 725.54 937.90 1.000 r(A<->C){all} 0.140204 0.000029 0.130070 0.150542 0.139982 359.83 400.53 1.000 r(A<->G){all} 0.293884 0.000122 0.272647 0.315905 0.293965 188.18 229.66 1.001 r(A<->T){all} 0.057949 0.000010 0.051737 0.063972 0.057912 515.89 534.92 1.002 r(C<->G){all} 0.075049 0.000025 0.066333 0.085532 0.074964 513.08 518.68 1.000 r(C<->T){all} 0.346683 0.000138 0.322485 0.368127 0.346471 213.59 254.69 1.000 r(G<->T){all} 0.086231 0.000019 0.078018 0.094919 0.086117 319.48 512.36 1.000 pi(A){all} 0.386740 0.000050 0.373746 0.401851 0.386734 210.01 306.33 1.000 pi(C){all} 0.171359 0.000025 0.161050 0.180935 0.171201 222.58 276.30 1.000 pi(G){all} 0.223939 0.000032 0.213688 0.236077 0.223881 286.80 398.06 1.000 pi(T){all} 0.217963 0.000034 0.206475 0.228823 0.218059 250.17 295.42 1.002 alpha{1,2} 0.526158 0.000651 0.476424 0.576596 0.525885 761.31 828.68 1.000 alpha{3} 1.140026 0.005302 1.004860 1.285954 1.137690 1501.00 1501.00 1.000 pinvar{all} 0.195264 0.000192 0.167768 0.220886 0.195251 672.47 836.32 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 -41627.237145 Model 2: PositiveSelection -40951.781415 Model 0: one-ratio -44297.988777 Model 3: discrete -40933.806577 Model 7: beta -41448.205743 Model 8: beta&w>1 -40858.949282 Model 0 vs 1 5341.503263999999 Model 2 vs 1 1350.911460000003 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.08.499_F5a.JQ777160_) Pr(w>1) post mean +- SE for w 10 C 1.000** 3.419 12 Q 0.944 3.284 13 W 0.591 2.430 18 I 0.741 2.792 27 G 0.977* 3.364 79 H 1.000** 3.419 125 T 0.890 3.153 126 D 1.000** 3.419 127 N 1.000** 3.419 128 T 1.000** 3.419 137 A 1.000** 3.419 140 E 0.530 2.282 145 K 0.999** 3.417 148 T 0.994** 3.404 160 S 0.999** 3.417 161 N 1.000** 3.419 162 S 1.000** 3.419 163 E 0.978* 3.366 173 T 1.000** 3.419 182 T 0.961* 3.325 205 T 0.534 2.291 213 N 0.558 2.351 249 L 0.783 2.895 255 T 0.942 3.280 263 S 0.958* 3.318 265 P 1.000** 3.419 272 N 1.000** 3.419 280 R 0.995** 3.408 287 F 0.865 3.094 289 D 1.000** 3.419 304 S 1.000** 3.419 305 A 1.000** 3.419 308 K 1.000** 3.419 311 E 1.000** 3.419 312 R 1.000** 3.419 314 K 1.000** 3.419 315 K 1.000** 3.419 318 G 0.586 2.419 320 Y 0.650 2.573 326 D 1.000** 3.419 328 Q 0.987* 3.387 329 P 1.000** 3.419 330 A 0.956* 3.313 355 K 1.000** 3.419 361 N 0.997** 3.413 362 T 1.000** 3.419 363 E 1.000** 3.419 364 N 1.000** 3.419 365 N 1.000** 3.419 366 S 1.000** 3.419 367 T 0.849 3.053 394 A 1.000** 3.419 396 N 1.000** 3.419 400 V 1.000** 3.418 414 V 1.000** 3.419 415 N 1.000** 3.419 416 N 1.000** 3.419 417 N 1.000** 3.419 418 T 1.000** 3.419 453 E 0.996** 3.411 467 I 0.943 3.282 517 M 0.615 2.489 564 S 1.000** 3.419 570 S 0.629 2.523 571 I 1.000** 3.419 572 D 1.000** 3.419 573 E 1.000** 3.419 591 H 1.000** 3.419 592 T 1.000** 3.419 595 R 1.000** 3.419 625 N 1.000** 3.419 628 K 0.952* 3.304 671 L 0.954* 3.309 672 T 1.000** 3.419 674 N 1.000** 3.419 675 P 0.996** 3.411 697 I 1.000** 3.419 701 S 1.000** 3.418 730 T 0.608 2.470 743 T 1.000** 3.419 747 L 0.787 2.904 752 Q 0.989* 3.393 784 V 0.924 3.236 787 I 1.000** 3.419 788 F 1.000** 3.419 792 C 1.000** 3.419 802 F 0.993** 3.403 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.08.499_F5a.JQ777160_) Pr(w>1) post mean +- SE for w 10 C 1.000** 3.500 +- 0.002 12 Q 0.944 3.360 +- 0.575 13 W 0.597 2.494 +- 1.226 18 I 0.734 2.836 +- 1.104 27 G 0.976* 3.440 +- 0.382 79 H 1.000** 3.500 +- 0.000 125 T 0.885 3.213 +- 0.797 126 D 1.000** 3.500 +- 0.024 127 N 1.000** 3.500 +- 0.000 128 T 1.000** 3.500 +- 0.000 137 A 1.000** 3.500 +- 0.009 140 E 0.506 2.265 +- 1.250 145 K 0.999** 3.498 +- 0.069 148 T 0.994** 3.485 +- 0.195 160 S 0.999** 3.498 +- 0.072 161 N 1.000** 3.500 +- 0.000 162 S 1.000** 3.500 +- 0.002 163 E 0.977* 3.444 +- 0.371 173 T 1.000** 3.500 +- 0.002 182 T 0.964* 3.410 +- 0.467 205 T 0.511 2.278 +- 1.250 213 N 0.540 2.350 +- 1.246 249 L 0.786 2.966 +- 1.024 255 T 0.941 3.354 +- 0.587 263 S 0.959* 3.398 +- 0.495 265 P 1.000** 3.500 +- 0.002 272 N 1.000** 3.500 +- 0.027 280 R 0.995** 3.489 +- 0.169 287 F 0.862 3.154 +- 0.863 289 D 1.000** 3.500 +- 0.001 304 S 1.000** 3.500 +- 0.000 305 A 1.000** 3.500 +- 0.001 308 K 1.000** 3.499 +- 0.040 311 E 1.000** 3.500 +- 0.001 312 R 1.000** 3.500 +- 0.000 314 K 1.000** 3.500 +- 0.020 315 K 1.000** 3.500 +- 0.001 318 G 0.561 2.403 +- 1.241 320 Y 0.644 2.609 +- 1.197 326 D 1.000** 3.500 +- 0.000 328 Q 0.986* 3.465 +- 0.296 329 P 1.000** 3.500 +- 0.017 330 A 0.959* 3.398 +- 0.493 355 K 1.000** 3.500 +- 0.000 361 N 0.998** 3.494 +- 0.124 362 T 1.000** 3.500 +- 0.000 363 E 1.000** 3.500 +- 0.000 364 N 1.000** 3.500 +- 0.006 365 N 1.000** 3.499 +- 0.040 366 S 1.000** 3.500 +- 0.000 367 T 0.844 3.110 +- 0.907 394 A 1.000** 3.500 +- 0.001 396 N 1.000** 3.500 +- 0.000 400 V 1.000** 3.499 +- 0.052 414 V 1.000** 3.500 +- 0.000 415 N 1.000** 3.500 +- 0.000 416 N 1.000** 3.500 +- 0.000 417 N 1.000** 3.500 +- 0.000 418 T 1.000** 3.500 +- 0.025 453 E 0.996** 3.491 +- 0.149 467 I 0.942 3.356 +- 0.583 517 M 0.625 2.562 +- 1.211 564 S 1.000** 3.500 +- 0.023 570 S 0.624 2.561 +- 1.211 571 I 1.000** 3.500 +- 0.000 572 D 1.000** 3.500 +- 0.003 573 E 1.000** 3.500 +- 0.006 591 H 1.000** 3.500 +- 0.000 592 T 1.000** 3.500 +- 0.009 595 R 1.000** 3.500 +- 0.000 625 N 1.000** 3.500 +- 0.009 628 K 0.950* 3.376 +- 0.544 671 L 0.956* 3.389 +- 0.514 672 T 1.000** 3.500 +- 0.000 674 N 1.000** 3.500 +- 0.001 675 P 0.997** 3.492 +- 0.141 697 I 1.000** 3.500 +- 0.003 701 S 1.000** 3.499 +- 0.049 730 T 0.595 2.488 +- 1.227 743 T 1.000** 3.500 +- 0.000 747 L 0.797 2.992 +- 1.006 752 Q 0.990** 3.475 +- 0.247 784 V 0.922 3.306 +- 0.669 787 I 1.000** 3.500 +- 0.001 788 F 1.000** 3.500 +- 0.000 792 C 1.000** 3.500 +- 0.004 802 F 0.994** 3.484 +- 0.199 Model 8 vs 7 1178.5129219999944 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.08.499_F5a.JQ777160_) Pr(w>1) post mean +- SE for w 10 C 1.000** 2.969 12 Q 0.939 2.845 13 W 0.630 2.215 18 I 0.748 2.459 27 G 0.969* 2.907 79 H 1.000** 2.969 125 T 0.884 2.734 126 D 1.000** 2.968 127 N 1.000** 2.969 128 T 1.000** 2.969 137 A 1.000** 2.969 140 E 0.515 1.993 145 K 0.999** 2.967 148 T 0.992** 2.953 160 S 0.998** 2.966 161 N 1.000** 2.969 162 S 1.000** 2.969 163 E 0.972* 2.913 173 T 1.000** 2.969 182 T 0.966* 2.899 205 T 0.537 2.034 213 N 0.550 2.063 249 L 0.795 2.552 255 T 0.944 2.855 263 S 0.959* 2.887 265 P 1.000** 2.969 272 N 1.000** 2.968 280 R 0.993** 2.955 287 F 0.864 2.694 289 D 1.000** 2.969 304 S 1.000** 2.969 305 A 1.000** 2.969 308 K 0.999** 2.968 311 E 1.000** 2.969 312 R 1.000** 2.969 314 K 1.000** 2.968 315 K 1.000** 2.969 318 G 0.566 2.096 320 Y 0.657 2.274 326 D 1.000** 2.969 328 Q 0.979* 2.927 329 P 1.000** 2.969 330 A 0.962* 2.892 355 K 1.000** 2.969 361 N 0.997** 2.962 362 T 1.000** 2.969 363 E 1.000** 2.969 364 N 1.000** 2.969 365 N 0.999** 2.968 366 S 1.000** 2.969 367 T 0.845 2.656 394 A 1.000** 2.969 396 N 1.000** 2.969 400 V 0.999** 2.967 414 V 1.000** 2.969 415 N 1.000** 2.969 416 N 1.000** 2.969 417 N 1.000** 2.969 418 T 1.000** 2.968 453 E 0.995** 2.959 467 I 0.935 2.839 517 M 0.656 2.268 564 S 1.000** 2.968 570 S 0.678 2.316 571 I 1.000** 2.969 572 D 1.000** 2.969 573 E 1.000** 2.969 587 S 0.506 1.973 591 H 1.000** 2.969 592 T 1.000** 2.969 595 R 1.000** 2.969 625 N 1.000** 2.969 628 K 0.941 2.851 671 L 0.957* 2.882 672 T 1.000** 2.969 674 N 1.000** 2.969 675 P 0.996** 2.961 697 I 1.000** 2.969 701 S 0.999** 2.967 707 F 0.502 1.956 730 T 0.669 2.300 743 T 1.000** 2.969 747 L 0.797 2.554 752 Q 0.987* 2.942 784 V 0.919 2.806 787 I 1.000** 2.969 788 F 1.000** 2.969 792 C 1.000** 2.969 802 F 0.990** 2.949 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.08.499_F5a.JQ777160_) Pr(w>1) post mean +- SE for w 7 K 0.691 2.009 +- 0.734 10 C 1.000** 2.500 +- 0.015 12 Q 0.987* 2.480 +- 0.179 13 W 0.887 2.320 +- 0.505 18 I 0.950* 2.422 +- 0.343 27 G 0.996** 2.494 +- 0.103 59 V 0.587 1.848 +- 0.778 79 H 1.000** 2.500 +- 0.015 125 T 0.982* 2.472 +- 0.210 126 D 1.000** 2.500 +- 0.018 127 N 1.000** 2.500 +- 0.015 128 T 1.000** 2.500 +- 0.015 137 A 1.000** 2.500 +- 0.016 140 E 0.921 2.377 +- 0.422 145 K 0.999** 2.499 +- 0.041 148 T 0.998** 2.497 +- 0.070 160 S 1.000** 2.500 +- 0.029 161 N 1.000** 2.500 +- 0.015 162 S 1.000** 2.500 +- 0.015 163 E 0.995** 2.493 +- 0.108 173 T 1.000** 2.500 +- 0.015 182 T 0.988* 2.482 +- 0.169 205 T 0.921 2.376 +- 0.424 211 P 0.569 1.818 +- 0.785 213 N 0.924 2.380 +- 0.417 249 L 0.947 2.416 +- 0.356 255 T 0.989* 2.483 +- 0.163 263 S 0.990** 2.485 +- 0.156 265 P 1.000** 2.500 +- 0.015 272 N 1.000** 2.500 +- 0.021 280 R 0.998** 2.498 +- 0.064 287 F 0.975* 2.461 +- 0.245 289 D 1.000** 2.500 +- 0.015 303 R 0.649 1.949 +- 0.750 304 S 1.000** 2.500 +- 0.015 305 A 1.000** 2.500 +- 0.015 308 K 1.000** 2.500 +- 0.023 311 E 1.000** 2.500 +- 0.015 312 R 1.000** 2.500 +- 0.015 314 K 1.000** 2.500 +- 0.019 315 K 1.000** 2.500 +- 0.015 318 G 0.937 2.402 +- 0.380 320 Y 0.926 2.383 +- 0.415 326 D 1.000** 2.500 +- 0.015 328 Q 0.997** 2.496 +- 0.083 329 P 1.000** 2.500 +- 0.018 330 A 0.987* 2.479 +- 0.181 355 K 1.000** 2.500 +- 0.015 361 N 0.999** 2.498 +- 0.061 362 T 1.000** 2.500 +- 0.015 363 E 1.000** 2.500 +- 0.015 364 N 1.000** 2.500 +- 0.016 365 N 1.000** 2.500 +- 0.023 366 S 1.000** 2.500 +- 0.015 367 T 0.973* 2.458 +- 0.254 394 A 1.000** 2.500 +- 0.015 396 N 1.000** 2.500 +- 0.015 400 V 1.000** 2.500 +- 0.027 414 V 1.000** 2.500 +- 0.015 415 N 1.000** 2.500 +- 0.015 416 N 1.000** 2.500 +- 0.015 417 N 1.000** 2.500 +- 0.015 418 T 1.000** 2.500 +- 0.022 453 E 0.999** 2.499 +- 0.054 467 I 0.989* 2.483 +- 0.165 487 I 0.731 2.077 +- 0.697 517 M 0.891 2.327 +- 0.496 559 N 0.835 2.241 +- 0.585 564 S 1.000** 2.500 +- 0.020 570 S 0.926 2.384 +- 0.413 571 I 1.000** 2.500 +- 0.015 572 D 1.000** 2.500 +- 0.015 573 E 1.000** 2.500 +- 0.016 587 S 0.925 2.382 +- 0.414 591 H 1.000** 2.500 +- 0.015 592 T 1.000** 2.500 +- 0.016 595 R 1.000** 2.500 +- 0.015 625 N 1.000** 2.500 +- 0.016 628 K 0.992** 2.487 +- 0.143 671 L 0.989* 2.482 +- 0.167 672 T 1.000** 2.500 +- 0.015 674 N 1.000** 2.500 +- 0.015 675 P 0.998** 2.498 +- 0.067 697 I 1.000** 2.500 +- 0.016 701 S 1.000** 2.500 +- 0.026 707 F 0.870 2.295 +- 0.532 709 D 0.634 1.921 +- 0.764 721 R 0.618 1.885 +- 0.784 730 T 0.936 2.399 +- 0.387 743 T 1.000** 2.500 +- 0.015 747 L 0.932 2.392 +- 0.401 752 Q 0.995** 2.492 +- 0.114 766 L 0.645 1.936 +- 0.762 783 I 0.755 2.114 +- 0.677 784 V 0.986* 2.479 +- 0.182 787 I 1.000** 2.500 +- 0.015 788 F 1.000** 2.500 +- 0.015 792 C 1.000** 2.500 +- 0.016 802 F 0.997** 2.496 +- 0.087