--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Jan 26 01:38:09 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_N1/ENV_1_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_4/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_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -47574.84 -47619.35 2 -47575.23 -47618.20 -------------------------------------- TOTAL -47575.02 -47618.93 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_4/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_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 7.748828 0.046437 7.351036 8.165507 7.745057 1022.37 1037.23 1.000 r(A<->C){all} 0.130021 0.000025 0.120680 0.139947 0.129875 429.33 460.64 1.002 r(A<->G){all} 0.302603 0.000117 0.280696 0.322816 0.302699 235.43 263.58 1.014 r(A<->T){all} 0.060401 0.000010 0.054216 0.066392 0.060381 506.54 673.28 1.000 r(C<->G){all} 0.069583 0.000025 0.059879 0.079438 0.069256 434.43 473.34 1.002 r(C<->T){all} 0.339722 0.000133 0.318179 0.362378 0.339234 247.05 307.01 1.017 r(G<->T){all} 0.097670 0.000023 0.088453 0.107563 0.097525 287.68 470.99 1.003 pi(A){all} 0.387628 0.000047 0.374024 0.400839 0.387767 454.91 455.51 1.000 pi(C){all} 0.182606 0.000024 0.172544 0.191875 0.182592 342.98 402.93 1.008 pi(G){all} 0.213580 0.000029 0.202984 0.224087 0.213451 356.18 377.00 1.017 pi(T){all} 0.216186 0.000035 0.205095 0.228336 0.216252 371.90 396.89 1.005 alpha{1,2} 0.467455 0.000489 0.426679 0.511776 0.466613 1148.31 1172.51 1.000 alpha{3} 1.074649 0.005165 0.944838 1.223442 1.070980 1013.18 1226.76 1.000 pinvar{all} 0.175622 0.000208 0.147828 0.202891 0.175615 1041.35 1121.90 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 -37442.164166 Model 2: PositiveSelection -36887.367584 Model 0: one-ratio -39726.536894 Model 3: discrete -36879.498558 Model 7: beta -37287.202195 Model 8: beta&w>1 -36784.671892 Model 0 vs 1 4568.74545599999 Model 2 vs 1 1109.5931640000053 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 02_AG.US.01.APV_12.DQ869018_) Pr(w>1) post mean +- SE for w 7 Y 1.000** 3.581 9 C 0.852 3.201 12 I 0.883 3.281 74 H 1.000** 3.582 120 Q 1.000** 3.582 121 D 0.985* 3.543 122 F 1.000** 3.582 123 M 1.000** 3.582 132 I 0.998** 3.577 140 R 1.000** 3.582 154 D 0.673 2.738 155 S 1.000** 3.582 165 A 0.846 3.184 247 T 0.555 2.432 257 K 0.997** 3.574 264 G 0.968* 3.499 272 R 1.000** 3.582 283 D 1.000** 3.582 297 K 0.764 2.971 298 A 1.000** 3.582 299 Q 1.000** 3.582 302 K 1.000** 3.582 305 Q 1.000** 3.582 306 E 1.000** 3.582 308 A 1.000** 3.582 309 K 1.000** 3.582 319 N 1.000** 3.582 321 N 1.000** 3.582 322 K 1.000** 3.581 348 A 1.000** 3.582 352 T 1.000** 3.582 353 I 1.000** 3.582 355 D 1.000** 3.582 382 A 1.000** 3.582 384 E 1.000** 3.582 388 E 0.987* 3.548 402 N 1.000** 3.582 403 S 0.785 3.027 438 R 0.787 3.033 543 D 0.728 2.881 548 S 0.998** 3.576 554 Y 1.000** 3.582 555 N 1.000** 3.582 556 D 0.617 2.592 572 S 1.000** 3.582 601 S 1.000** 3.582 647 P 0.841 3.171 648 T 1.000** 3.581 650 H 1.000** 3.581 651 Q 0.999** 3.580 673 V 1.000** 3.582 683 A 1.000** 3.582 697 R 0.703 2.814 711 A 0.979* 3.526 720 S 0.839 3.166 747 I 0.726 2.875 751 T 0.999** 3.580 752 G 0.965* 3.492 756 R 0.996** 3.571 766 L 0.998** 3.575 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: 02_AG.US.01.APV_12.DQ869018_) Pr(w>1) post mean +- SE for w 7 Y 1.000** 3.500 +- 0.027 9 C 0.877 3.191 +- 0.822 12 I 0.901 3.254 +- 0.745 74 H 1.000** 3.500 +- 0.001 120 Q 1.000** 3.500 +- 0.000 121 D 0.988* 3.471 +- 0.267 122 F 1.000** 3.500 +- 0.000 123 M 1.000** 3.500 +- 0.000 132 I 0.999** 3.496 +- 0.095 140 R 1.000** 3.500 +- 0.017 154 D 0.740 2.849 +- 1.097 155 S 1.000** 3.500 +- 0.000 165 A 0.866 3.165 +- 0.852 247 T 0.616 2.539 +- 1.216 257 K 0.997** 3.494 +- 0.127 264 G 0.974* 3.434 +- 0.400 272 R 1.000** 3.500 +- 0.002 283 D 1.000** 3.500 +- 0.002 297 K 0.814 3.034 +- 0.974 298 A 1.000** 3.500 +- 0.000 299 Q 1.000** 3.500 +- 0.000 302 K 1.000** 3.500 +- 0.001 305 Q 1.000** 3.500 +- 0.001 306 E 1.000** 3.500 +- 0.005 308 A 1.000** 3.500 +- 0.000 309 K 1.000** 3.500 +- 0.002 319 N 1.000** 3.500 +- 0.001 321 N 1.000** 3.500 +- 0.019 322 K 1.000** 3.499 +- 0.049 348 A 1.000** 3.500 +- 0.000 352 T 1.000** 3.500 +- 0.000 353 I 1.000** 3.500 +- 0.000 355 D 1.000** 3.500 +- 0.000 382 A 1.000** 3.500 +- 0.002 384 E 1.000** 3.500 +- 0.000 388 E 0.989* 3.473 +- 0.258 402 N 1.000** 3.500 +- 0.000 403 S 0.822 3.056 +- 0.956 438 R 0.826 3.066 +- 0.947 543 D 0.769 2.923 +- 1.053 548 S 0.998** 3.495 +- 0.111 554 Y 1.000** 3.500 +- 0.000 555 N 1.000** 3.500 +- 0.000 556 D 0.679 2.698 +- 1.167 572 S 1.000** 3.500 +- 0.000 601 S 1.000** 3.500 +- 0.002 647 P 0.862 3.156 +- 0.861 648 T 1.000** 3.500 +- 0.035 650 H 1.000** 3.499 +- 0.052 651 Q 0.999** 3.499 +- 0.056 673 V 1.000** 3.500 +- 0.002 683 A 1.000** 3.500 +- 0.004 697 R 0.734 2.834 +- 1.105 711 A 0.981* 3.453 +- 0.339 720 S 0.857 3.143 +- 0.875 747 I 0.781 2.952 +- 1.034 751 T 0.999** 3.498 +- 0.061 752 G 0.970* 3.425 +- 0.426 756 R 0.996** 3.491 +- 0.154 766 L 0.998** 3.494 +- 0.118 Model 8 vs 7 1005.0606059999991 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 02_AG.US.01.APV_12.DQ869018_) Pr(w>1) post mean +- SE for w 7 Y 1.000** 3.160 9 C 0.865 2.862 12 I 0.899 2.936 74 H 1.000** 3.160 120 Q 1.000** 3.160 121 D 0.982* 3.121 122 F 1.000** 3.160 123 M 1.000** 3.160 132 I 0.998** 3.155 140 R 1.000** 3.160 154 D 0.674 2.444 155 S 1.000** 3.160 165 A 0.877 2.888 247 T 0.633 2.349 257 K 0.996** 3.150 264 G 0.968* 3.089 272 R 1.000** 3.160 283 D 1.000** 3.160 297 K 0.783 2.683 298 A 1.000** 3.160 299 Q 1.000** 3.160 302 K 1.000** 3.160 305 Q 1.000** 3.160 306 E 1.000** 3.160 308 A 1.000** 3.160 309 K 1.000** 3.160 319 N 1.000** 3.160 321 N 1.000** 3.160 322 K 0.999** 3.159 348 A 1.000** 3.160 352 T 1.000** 3.160 353 I 1.000** 3.160 355 D 1.000** 3.160 382 A 1.000** 3.160 384 E 1.000** 3.160 388 E 0.986* 3.129 402 N 1.000** 3.160 403 S 0.795 2.707 438 R 0.810 2.742 543 D 0.773 2.658 548 S 0.998** 3.155 554 Y 1.000** 3.160 555 N 1.000** 3.160 556 D 0.648 2.385 572 S 1.000** 3.160 601 S 1.000** 3.160 647 P 0.871 2.874 648 T 1.000** 3.159 650 H 0.999** 3.159 651 Q 0.999** 3.159 673 V 1.000** 3.160 683 A 1.000** 3.160 697 R 0.756 2.617 711 A 0.982* 3.120 720 S 0.851 2.829 747 I 0.753 2.617 751 T 0.999** 3.158 752 G 0.968* 3.089 756 R 0.996** 3.151 766 L 0.997** 3.153 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: 02_AG.US.01.APV_12.DQ869018_) Pr(w>1) post mean +- SE for w 7 Y 1.000** 3.499 +- 0.042 9 C 0.618 2.519 +- 1.249 12 I 0.713 2.761 +- 1.164 74 H 1.000** 3.500 +- 0.001 120 Q 1.000** 3.500 +- 0.001 121 D 0.924 3.306 +- 0.677 122 F 1.000** 3.500 +- 0.001 123 M 1.000** 3.500 +- 0.001 132 I 0.993** 3.483 +- 0.210 140 R 1.000** 3.500 +- 0.033 155 S 1.000** 3.500 +- 0.001 165 A 0.689 2.700 +- 1.192 257 K 0.985* 3.463 +- 0.306 264 G 0.891 3.220 +- 0.800 272 R 1.000** 3.500 +- 0.003 283 D 1.000** 3.500 +- 0.004 298 A 1.000** 3.500 +- 0.001 299 Q 1.000** 3.500 +- 0.001 302 K 1.000** 3.500 +- 0.002 305 Q 1.000** 3.500 +- 0.002 306 E 1.000** 3.500 +- 0.008 308 A 1.000** 3.500 +- 0.001 309 K 1.000** 3.500 +- 0.003 319 N 1.000** 3.500 +- 0.002 321 N 1.000** 3.499 +- 0.039 322 K 0.998** 3.496 +- 0.102 348 A 1.000** 3.500 +- 0.001 352 T 1.000** 3.500 +- 0.001 353 I 1.000** 3.500 +- 0.001 355 D 1.000** 3.500 +- 0.001 382 A 1.000** 3.500 +- 0.004 384 E 1.000** 3.500 +- 0.001 388 E 0.953* 3.379 +- 0.544 402 N 1.000** 3.500 +- 0.001 548 S 0.995** 3.488 +- 0.178 554 Y 1.000** 3.500 +- 0.001 555 N 1.000** 3.500 +- 0.001 572 S 1.000** 3.500 +- 0.001 601 S 1.000** 3.500 +- 0.004 647 P 0.668 2.645 +- 1.213 648 T 1.000** 3.499 +- 0.049 650 H 0.999** 3.497 +- 0.088 651 Q 0.999** 3.497 +- 0.084 673 V 1.000** 3.500 +- 0.004 683 A 1.000** 3.500 +- 0.005 711 A 0.953* 3.378 +- 0.546 720 S 0.654 2.608 +- 1.227 751 T 0.998** 3.495 +- 0.114 752 G 0.908 3.265 +- 0.741 756 R 0.992** 3.481 +- 0.223 766 L 0.993** 3.481 +- 0.218