--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Jan 25 09:11:05 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_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -47535.55 -47579.59 2 -47533.27 -47573.31 -------------------------------------- TOTAL -47533.87 -47578.89 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 8.147714 0.052385 7.729361 8.626980 8.139656 1076.76 1204.17 1.001 r(A<->C){all} 0.141654 0.000032 0.130391 0.152396 0.141447 401.70 411.87 1.000 r(A<->G){all} 0.291887 0.000102 0.272137 0.311162 0.291604 145.65 180.29 1.000 r(A<->T){all} 0.046725 0.000008 0.041422 0.052354 0.046612 323.12 464.97 1.000 r(C<->G){all} 0.075533 0.000024 0.066197 0.084946 0.075400 553.00 591.86 1.001 r(C<->T){all} 0.357902 0.000122 0.336487 0.379274 0.357698 160.72 168.28 1.000 r(G<->T){all} 0.086299 0.000022 0.076782 0.095107 0.086236 423.94 451.99 1.002 pi(A){all} 0.399936 0.000045 0.386726 0.412288 0.399934 290.39 292.73 1.000 pi(C){all} 0.165861 0.000024 0.156395 0.175030 0.165837 179.73 242.44 1.000 pi(G){all} 0.218510 0.000027 0.208984 0.228663 0.218562 292.20 298.88 1.000 pi(T){all} 0.215693 0.000035 0.204815 0.227487 0.215640 227.78 310.02 1.000 alpha{1,2} 0.477318 0.000529 0.433189 0.524312 0.476482 997.07 1084.58 1.000 alpha{3} 1.126482 0.004631 0.993516 1.259227 1.126366 1182.96 1268.03 1.000 pinvar{all} 0.195947 0.000190 0.169324 0.221458 0.195847 1151.71 1168.68 1.001 ------------------------------------------------------------------------------------------------------ * 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 -39250.562022 Model 2: PositiveSelection -38585.194973 Model 0: one-ratio -41788.41876 Model 3: discrete -38541.392658 Model 7: beta -39026.033037 Model 8: beta&w>1 -38448.428616 Model 0 vs 1 5075.713476000004 Model 2 vs 1 1330.7340980000008 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.03.03ZAPS133MB1.DQ275646_) Pr(w>1) post mean +- SE for w 4 K 0.981* 3.536 7 Q 0.846 3.186 14 M 0.976* 3.523 55 E 0.956* 3.471 78 V 1.000** 3.584 125 T 1.000** 3.584 127 A 1.000** 3.584 135 T 0.999** 3.581 142 K 1.000** 3.583 145 Y 0.559 2.445 155 P 0.996** 3.573 157 N 1.000** 3.584 158 G 1.000** 3.584 159 N 1.000** 3.584 160 S 1.000** 3.584 179 S 0.897 3.317 246 L 0.878 3.268 260 S 0.938 3.423 262 Q 1.000** 3.584 264 V 0.997** 3.577 277 R 1.000** 3.584 299 D 1.000** 3.584 300 Q 0.998** 3.578 303 R 0.745 2.925 306 E 1.000** 3.584 307 Q 1.000** 3.584 309 K 1.000** 3.584 310 K 1.000** 3.584 313 G 1.000** 3.584 315 H 0.999** 3.580 319 L 1.000** 3.584 321 A 1.000** 3.584 322 P 0.987* 3.550 323 A 1.000** 3.584 348 N 1.000** 3.584 351 K 1.000** 3.584 352 S 1.000** 3.584 353 D 1.000** 3.583 354 E 1.000** 3.584 382 E 1.000** 3.583 384 N 1.000** 3.584 386 T 0.680 2.756 388 N 1.000** 3.584 402 R 1.000** 3.584 403 N 1.000** 3.583 404 D 1.000** 3.584 405 T 1.000** 3.584 440 T 0.796 3.058 544 A 1.000** 3.583 549 S 1.000** 3.583 555 Q 1.000** 3.584 556 T 1.000** 3.584 557 D 1.000** 3.583 560 D 1.000** 3.584 572 N 0.872 3.252 576 G 1.000** 3.584 577 T 1.000** 3.584 580 R 1.000** 3.584 610 D 0.987* 3.551 657 T 1.000** 3.584 659 N 1.000** 3.583 660 P 0.995** 3.570 682 V 1.000** 3.583 686 S 0.959* 3.477 692 A 1.000** 3.584 719 H 0.999** 3.582 724 A 1.000** 3.583 733 Q 0.868 3.241 760 V 0.991** 3.560 761 I 0.855 3.209 764 I 0.990* 3.557 765 C 1.000** 3.584 769 S 1.000** 3.584 779 F 0.985* 3.545 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.03.03ZAPS133MB1.DQ275646_) Pr(w>1) post mean +- SE for w 4 K 0.981* 3.454 +- 0.338 7 Q 0.845 3.112 +- 0.905 14 M 0.975* 3.438 +- 0.388 55 E 0.957* 3.392 +- 0.508 78 V 1.000** 3.500 +- 0.001 125 T 1.000** 3.500 +- 0.012 127 A 1.000** 3.500 +- 0.000 135 T 0.999** 3.498 +- 0.078 142 K 1.000** 3.499 +- 0.050 145 Y 0.581 2.452 +- 1.234 155 P 0.995** 3.489 +- 0.168 157 N 1.000** 3.500 +- 0.007 158 G 1.000** 3.500 +- 0.000 159 N 1.000** 3.500 +- 0.001 160 S 1.000** 3.500 +- 0.000 179 S 0.892 3.229 +- 0.777 246 L 0.870 3.176 +- 0.839 260 S 0.935 3.338 +- 0.615 262 Q 1.000** 3.500 +- 0.005 264 V 0.997** 3.493 +- 0.133 277 R 1.000** 3.500 +- 0.001 299 D 1.000** 3.500 +- 0.000 300 Q 0.998** 3.495 +- 0.114 303 R 0.763 2.909 +- 1.062 306 E 1.000** 3.500 +- 0.000 307 Q 1.000** 3.500 +- 0.000 309 K 1.000** 3.500 +- 0.000 310 K 1.000** 3.500 +- 0.000 313 G 1.000** 3.500 +- 0.018 315 H 0.999** 3.497 +- 0.093 319 L 1.000** 3.500 +- 0.000 321 A 1.000** 3.500 +- 0.006 322 P 0.986* 3.466 +- 0.290 323 A 1.000** 3.500 +- 0.007 348 N 1.000** 3.500 +- 0.001 351 K 1.000** 3.500 +- 0.000 352 S 1.000** 3.500 +- 0.000 353 D 1.000** 3.499 +- 0.043 354 E 1.000** 3.500 +- 0.000 382 E 1.000** 3.500 +- 0.026 384 N 1.000** 3.500 +- 0.000 386 T 0.702 2.756 +- 1.143 388 N 1.000** 3.500 +- 0.011 402 R 1.000** 3.500 +- 0.000 403 N 1.000** 3.500 +- 0.031 404 D 1.000** 3.500 +- 0.000 405 T 1.000** 3.500 +- 0.004 440 T 0.806 3.015 +- 0.989 544 A 1.000** 3.500 +- 0.020 549 S 1.000** 3.499 +- 0.045 555 Q 1.000** 3.500 +- 0.000 556 T 1.000** 3.500 +- 0.000 557 D 1.000** 3.499 +- 0.043 560 D 1.000** 3.500 +- 0.010 572 N 0.879 3.197 +- 0.816 576 G 1.000** 3.500 +- 0.000 577 T 1.000** 3.500 +- 0.001 580 R 1.000** 3.500 +- 0.000 610 D 0.987* 3.468 +- 0.279 657 T 1.000** 3.500 +- 0.000 659 N 1.000** 3.500 +- 0.034 660 P 0.994** 3.485 +- 0.191 682 V 1.000** 3.499 +- 0.050 686 S 0.959* 3.397 +- 0.496 692 A 1.000** 3.500 +- 0.013 719 H 0.999** 3.498 +- 0.073 724 A 1.000** 3.499 +- 0.051 733 Q 0.860 3.151 +- 0.867 760 V 0.990** 3.476 +- 0.243 761 I 0.858 3.145 +- 0.872 764 I 0.989* 3.473 +- 0.260 765 C 1.000** 3.500 +- 0.000 769 S 1.000** 3.500 +- 0.014 779 F 0.984* 3.460 +- 0.313 Model 8 vs 7 1155.2088420000073 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.03.03ZAPS133MB1.DQ275646_) Pr(w>1) post mean +- SE for w 4 K 0.977* 3.015 7 Q 0.850 2.744 14 M 0.975* 3.010 55 E 0.949 2.954 78 V 1.000** 3.062 125 T 1.000** 3.062 127 A 1.000** 3.062 135 T 0.998** 3.059 142 K 0.999** 3.061 145 Y 0.605 2.223 155 P 0.994** 3.050 157 N 1.000** 3.062 158 G 1.000** 3.062 159 N 1.000** 3.062 160 S 1.000** 3.062 179 S 0.916 2.884 246 L 0.887 2.821 260 S 0.945 2.946 262 Q 1.000** 3.062 264 V 0.995** 3.051 277 R 1.000** 3.062 299 D 1.000** 3.062 300 Q 0.996** 3.054 303 R 0.721 2.474 306 E 1.000** 3.062 307 Q 1.000** 3.062 309 K 1.000** 3.062 310 K 1.000** 3.062 313 G 1.000** 3.062 315 H 0.998** 3.059 319 L 1.000** 3.062 321 A 1.000** 3.062 322 P 0.984* 3.028 323 A 1.000** 3.062 348 N 1.000** 3.062 351 K 1.000** 3.062 352 S 1.000** 3.062 353 D 0.999** 3.061 354 E 1.000** 3.062 382 E 1.000** 3.062 384 N 1.000** 3.062 386 T 0.647 2.316 388 N 1.000** 3.062 402 R 1.000** 3.062 403 N 1.000** 3.062 404 D 1.000** 3.062 405 T 1.000** 3.062 440 T 0.801 2.641 544 A 1.000** 3.062 549 S 1.000** 3.062 555 Q 1.000** 3.062 556 T 1.000** 3.062 557 D 0.999** 3.061 560 D 1.000** 3.062 572 N 0.856 2.758 576 G 1.000** 3.062 577 T 1.000** 3.062 580 R 1.000** 3.062 610 D 0.983* 3.027 657 T 1.000** 3.062 659 N 1.000** 3.062 660 P 0.994** 3.050 682 V 0.999** 3.061 686 S 0.953* 2.962 692 A 1.000** 3.062 719 H 0.999** 3.060 724 A 1.000** 3.061 733 Q 0.867 2.778 760 V 0.988* 3.038 761 I 0.845 2.736 764 I 0.988* 3.037 765 C 1.000** 3.062 769 S 1.000** 3.062 779 F 0.981* 3.022 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.03.03ZAPS133MB1.DQ275646_) Pr(w>1) post mean +- SE for w 4 K 0.841 3.092 +- 0.936 14 M 0.865 3.155 +- 0.874 55 E 0.681 2.682 +- 1.193 78 V 1.000** 3.499 +- 0.023 125 T 1.000** 3.499 +- 0.038 127 A 1.000** 3.499 +- 0.023 135 T 0.989* 3.471 +- 0.271 142 K 0.995** 3.487 +- 0.178 155 P 0.967* 3.415 +- 0.458 157 N 1.000** 3.499 +- 0.034 158 G 1.000** 3.499 +- 0.023 159 N 1.000** 3.499 +- 0.023 160 S 1.000** 3.499 +- 0.023 179 S 0.680 2.678 +- 1.198 246 L 0.620 2.524 +- 1.247 260 S 0.745 2.844 +- 1.118 262 Q 1.000** 3.499 +- 0.027 264 V 0.967* 3.415 +- 0.458 277 R 1.000** 3.499 +- 0.023 299 D 1.000** 3.499 +- 0.023 300 Q 0.975* 3.436 +- 0.399 306 E 1.000** 3.499 +- 0.023 307 Q 1.000** 3.499 +- 0.023 309 K 1.000** 3.499 +- 0.023 310 K 1.000** 3.499 +- 0.023 313 G 1.000** 3.498 +- 0.056 315 H 0.993** 3.481 +- 0.217 319 L 1.000** 3.499 +- 0.023 321 A 1.000** 3.499 +- 0.029 322 P 0.904 3.254 +- 0.754 323 A 1.000** 3.499 +- 0.025 348 N 1.000** 3.499 +- 0.023 351 K 1.000** 3.499 +- 0.023 352 S 1.000** 3.499 +- 0.023 353 D 0.996** 3.489 +- 0.167 354 E 1.000** 3.499 +- 0.023 382 E 0.999** 3.497 +- 0.084 384 N 1.000** 3.499 +- 0.023 388 N 1.000** 3.499 +- 0.035 402 R 1.000** 3.499 +- 0.023 403 N 0.999** 3.496 +- 0.097 404 D 1.000** 3.499 +- 0.023 405 T 1.000** 3.499 +- 0.025 544 A 1.000** 3.499 +- 0.049 549 S 0.999** 3.497 +- 0.090 555 Q 1.000** 3.499 +- 0.023 556 T 1.000** 3.499 +- 0.023 557 D 0.997** 3.493 +- 0.130 560 D 1.000** 3.499 +- 0.043 576 G 1.000** 3.499 +- 0.023 577 T 1.000** 3.499 +- 0.023 580 R 1.000** 3.499 +- 0.023 610 D 0.875 3.180 +- 0.845 657 T 1.000** 3.499 +- 0.023 659 N 0.999** 3.498 +- 0.074 660 P 0.979* 3.446 +- 0.367 682 V 0.997** 3.493 +- 0.134 686 S 0.702 2.736 +- 1.171 692 A 1.000** 3.499 +- 0.033 719 H 0.997** 3.493 +- 0.132 724 A 0.999** 3.496 +- 0.095 733 Q 0.561 2.371 +- 1.275 760 V 0.929 3.318 +- 0.656 764 I 0.928 3.315 +- 0.661 765 C 1.000** 3.499 +- 0.023 769 S 1.000** 3.499 +- 0.032 779 F 0.903 3.251 +- 0.758