--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Mar 16 18:08:41 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_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -49062.58 -49102.16 2 -49062.60 -49097.89 -------------------------------------- TOTAL -49062.59 -49101.48 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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} 8.327723 0.062764 7.838347 8.804613 8.323195 721.09 782.54 1.000 r(A<->C){all} 0.142434 0.000028 0.132260 0.152749 0.142495 379.58 487.51 1.001 r(A<->G){all} 0.284031 0.000124 0.262610 0.305678 0.283619 280.03 282.84 1.002 r(A<->T){all} 0.059054 0.000010 0.052999 0.065212 0.059008 482.02 509.82 1.003 r(C<->G){all} 0.074755 0.000026 0.064612 0.084583 0.074759 350.18 419.03 1.000 r(C<->T){all} 0.356884 0.000145 0.331768 0.379038 0.356876 287.44 299.18 1.003 r(G<->T){all} 0.082843 0.000021 0.073204 0.091287 0.082788 479.90 502.08 1.001 pi(A){all} 0.399460 0.000049 0.386136 0.413828 0.399375 291.57 366.11 1.006 pi(C){all} 0.164734 0.000025 0.155195 0.174894 0.164822 281.30 326.58 1.002 pi(G){all} 0.227160 0.000032 0.215584 0.237721 0.227137 362.23 394.57 1.000 pi(T){all} 0.208646 0.000034 0.196991 0.219576 0.208743 285.37 297.72 1.001 alpha{1,2} 0.474740 0.000535 0.432417 0.519954 0.473873 921.21 1003.63 1.000 alpha{3} 1.069343 0.004589 0.944083 1.203141 1.066979 1073.09 1089.85 1.000 pinvar{all} 0.173860 0.000209 0.145213 0.200875 0.174249 1111.26 1177.50 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 -40099.699125 Model 2: PositiveSelection -39449.807234 Model 0: one-ratio -42578.476225 Model 3: discrete -39424.72764 Model 7: beta -39913.947239 Model 8: beta&w>1 -39331.455117 Model 0 vs 1 4957.554199999999 Model 2 vs 1 1299.7837819999986 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.US.04.USPI71101EI7y04051pcWG2B9.JN024210_) Pr(w>1) post mean +- SE for w 51 A 0.766 2.981 74 K 1.000** 3.585 123 L 1.000** 3.585 124 E 1.000** 3.585 125 N 1.000** 3.585 126 T 1.000** 3.585 127 T 1.000** 3.585 128 N 1.000** 3.585 129 A 1.000** 3.585 130 A 1.000** 3.585 139 V 0.998** 3.580 146 M 0.996** 3.575 147 K 0.678 2.753 150 Y 0.995** 3.572 162 E 1.000** 3.585 163 D 1.000** 3.585 164 D 1.000** 3.585 174 I 0.954* 3.465 183 T 0.999** 3.582 214 R 0.814 3.104 251 K 0.982* 3.539 253 T 1.000** 3.585 265 V 0.991** 3.562 272 N 1.000** 3.585 280 H 0.995** 3.572 289 E 1.000** 3.585 296 Q 0.706 2.826 305 K 1.000** 3.584 308 E 0.976* 3.522 309 K 1.000** 3.585 311 V 1.000** 3.585 312 E 1.000** 3.585 315 R 0.998** 3.581 322 T 1.000** 3.585 324 K 0.998** 3.581 325 P 0.991** 3.561 326 S 1.000** 3.585 351 Q 1.000** 3.585 355 S 0.998** 3.579 357 D 1.000** 3.585 358 T 0.855 3.211 385 R 1.000** 3.585 387 Q 1.000** 3.585 391 S 0.765 2.978 405 V 1.000** 3.585 406 N 1.000** 3.585 407 T 1.000** 3.585 408 T 1.000** 3.585 443 K 1.000** 3.585 459 V 0.890 3.300 548 A 1.000** 3.585 553 A 1.000** 3.585 560 Q 1.000** 3.585 561 K 1.000** 3.585 562 Y 1.000** 3.585 580 D 1.000** 3.585 581 L 1.000** 3.585 584 N 1.000** 3.585 614 S 1.000** 3.585 661 L 1.000** 3.585 663 T 0.999** 3.583 686 G 1.000** 3.585 690 N 0.646 2.671 696 V 0.832 3.150 728 I 1.000** 3.585 751 L 0.700 2.808 772 V 1.000** 3.584 773 F 1.000** 3.585 779 L 0.513 2.326 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.US.04.USPI71101EI7y04051pcWG2B9.JN024210_) Pr(w>1) post mean +- SE for w 51 A 0.793 2.982 +- 1.013 74 K 1.000** 3.500 +- 0.001 123 L 1.000** 3.500 +- 0.000 124 E 1.000** 3.500 +- 0.000 125 N 1.000** 3.500 +- 0.000 126 T 1.000** 3.500 +- 0.000 127 T 1.000** 3.500 +- 0.000 128 N 1.000** 3.500 +- 0.000 129 A 1.000** 3.500 +- 0.000 130 A 1.000** 3.500 +- 0.000 139 V 0.998** 3.495 +- 0.109 146 M 0.996** 3.491 +- 0.151 147 K 0.681 2.704 +- 1.165 150 Y 0.995** 3.488 +- 0.176 162 E 1.000** 3.500 +- 0.001 163 D 1.000** 3.500 +- 0.000 164 D 1.000** 3.500 +- 0.013 174 I 0.954* 3.385 +- 0.524 183 T 0.999** 3.497 +- 0.090 214 R 0.833 3.082 +- 0.933 251 K 0.983* 3.458 +- 0.322 253 T 1.000** 3.500 +- 0.006 265 V 0.992** 3.480 +- 0.224 272 N 1.000** 3.500 +- 0.000 280 H 0.995** 3.488 +- 0.173 289 E 1.000** 3.500 +- 0.000 296 Q 0.725 2.813 +- 1.116 305 K 1.000** 3.499 +- 0.038 308 E 0.977* 3.443 +- 0.373 309 K 1.000** 3.500 +- 0.000 311 V 1.000** 3.500 +- 0.009 312 E 1.000** 3.500 +- 0.005 315 R 0.999** 3.496 +- 0.096 322 T 1.000** 3.500 +- 0.000 324 K 0.998** 3.496 +- 0.098 325 P 0.991** 3.478 +- 0.235 326 S 1.000** 3.500 +- 0.011 351 Q 1.000** 3.500 +- 0.000 355 S 0.998** 3.495 +- 0.112 357 D 1.000** 3.500 +- 0.000 358 T 0.865 3.162 +- 0.854 385 R 1.000** 3.500 +- 0.022 387 Q 1.000** 3.500 +- 0.000 391 S 0.785 2.963 +- 1.027 405 V 1.000** 3.500 +- 0.000 406 N 1.000** 3.500 +- 0.001 407 T 1.000** 3.500 +- 0.001 408 T 1.000** 3.500 +- 0.000 443 K 1.000** 3.500 +- 0.001 459 V 0.896 3.239 +- 0.764 548 A 1.000** 3.500 +- 0.011 553 A 1.000** 3.500 +- 0.019 560 Q 1.000** 3.500 +- 0.000 561 K 1.000** 3.500 +- 0.001 562 Y 1.000** 3.500 +- 0.013 580 D 1.000** 3.500 +- 0.000 581 L 1.000** 3.500 +- 0.013 584 N 1.000** 3.500 +- 0.000 614 S 1.000** 3.500 +- 0.013 661 L 1.000** 3.500 +- 0.010 663 T 0.999** 3.498 +- 0.067 686 G 1.000** 3.500 +- 0.024 690 N 0.681 2.703 +- 1.165 696 V 0.838 3.094 +- 0.922 728 I 1.000** 3.500 +- 0.002 751 L 0.714 2.785 +- 1.130 772 V 1.000** 3.499 +- 0.041 773 F 1.000** 3.500 +- 0.009 779 L 0.537 2.341 +- 1.247 Model 8 vs 7 1164.9842440000066 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.US.04.USPI71101EI7y04051pcWG2B9.JN024210_) Pr(w>1) post mean +- SE for w 51 A 0.773 2.616 74 K 1.000** 3.103 123 L 1.000** 3.103 124 E 1.000** 3.103 125 N 1.000** 3.103 126 T 1.000** 3.103 127 T 1.000** 3.103 128 N 1.000** 3.103 129 A 1.000** 3.103 130 A 1.000** 3.103 139 V 0.997** 3.098 146 M 0.994** 3.091 147 K 0.713 2.482 150 Y 0.994** 3.092 162 E 1.000** 3.103 163 D 1.000** 3.103 164 D 1.000** 3.103 174 I 0.962* 3.021 183 T 0.999** 3.101 214 R 0.807 2.689 251 K 0.979* 3.059 253 T 1.000** 3.103 265 V 0.989* 3.079 272 N 1.000** 3.103 280 H 0.994** 3.091 289 E 1.000** 3.103 296 Q 0.735 2.529 305 K 1.000** 3.103 308 E 0.970* 3.040 309 K 1.000** 3.103 311 V 1.000** 3.103 312 E 1.000** 3.103 315 R 0.998** 3.098 322 T 1.000** 3.103 324 K 0.997** 3.098 325 P 0.989* 3.081 326 S 1.000** 3.103 351 Q 1.000** 3.103 355 S 0.996** 3.096 357 D 1.000** 3.103 358 T 0.876 2.837 385 R 1.000** 3.103 387 Q 1.000** 3.103 391 S 0.785 2.640 405 V 1.000** 3.103 406 N 1.000** 3.103 407 T 1.000** 3.103 408 T 1.000** 3.103 443 K 1.000** 3.103 459 V 0.897 2.882 548 A 1.000** 3.103 553 A 1.000** 3.103 560 Q 1.000** 3.103 561 K 1.000** 3.103 562 Y 1.000** 3.103 580 D 1.000** 3.103 581 L 1.000** 3.103 584 N 1.000** 3.103 614 S 1.000** 3.103 661 L 1.000** 3.103 663 T 0.999** 3.102 686 G 1.000** 3.103 690 N 0.669 2.390 696 V 0.869 2.820 728 I 1.000** 3.103 751 L 0.749 2.561 772 V 1.000** 3.103 773 F 1.000** 3.103 779 L 0.556 2.140 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.US.04.USPI71101EI7y04051pcWG2B9.JN024210_) Pr(w>1) post mean +- SE for w 74 K 1.000** 3.499 +- 0.032 123 L 1.000** 3.499 +- 0.032 124 E 1.000** 3.499 +- 0.032 125 N 1.000** 3.499 +- 0.032 126 T 1.000** 3.499 +- 0.032 127 T 1.000** 3.499 +- 0.032 128 N 1.000** 3.499 +- 0.032 129 A 1.000** 3.499 +- 0.032 130 A 1.000** 3.499 +- 0.032 139 V 0.987* 3.466 +- 0.288 146 M 0.974* 3.433 +- 0.406 150 Y 0.977* 3.441 +- 0.382 162 E 1.000** 3.499 +- 0.033 163 D 1.000** 3.499 +- 0.032 164 D 1.000** 3.498 +- 0.048 174 I 0.860 3.140 +- 0.892 183 T 0.997** 3.491 +- 0.150 251 K 0.899 3.239 +- 0.774 253 T 1.000** 3.499 +- 0.034 265 V 0.936 3.334 +- 0.629 272 N 1.000** 3.499 +- 0.032 280 H 0.974* 3.433 +- 0.406 289 E 1.000** 3.499 +- 0.032 305 K 0.998** 3.495 +- 0.105 308 E 0.852 3.119 +- 0.911 309 K 1.000** 3.499 +- 0.032 311 V 1.000** 3.499 +- 0.037 312 E 1.000** 3.499 +- 0.035 315 R 0.989* 3.471 +- 0.269 322 T 1.000** 3.499 +- 0.032 324 K 0.989* 3.471 +- 0.269 325 P 0.949 3.367 +- 0.567 326 S 1.000** 3.499 +- 0.035 351 Q 1.000** 3.499 +- 0.032 355 S 0.982* 3.454 +- 0.338 357 D 1.000** 3.499 +- 0.032 358 T 0.549 2.341 +- 1.278 385 R 0.999** 3.497 +- 0.070 387 Q 1.000** 3.499 +- 0.032 405 V 1.000** 3.499 +- 0.032 406 N 1.000** 3.499 +- 0.032 407 T 1.000** 3.499 +- 0.033 408 T 1.000** 3.499 +- 0.032 443 K 1.000** 3.499 +- 0.032 459 V 0.616 2.512 +- 1.251 548 A 1.000** 3.499 +- 0.039 553 A 1.000** 3.499 +- 0.046 560 Q 1.000** 3.499 +- 0.032 561 K 1.000** 3.499 +- 0.032 562 Y 1.000** 3.499 +- 0.046 580 D 1.000** 3.499 +- 0.032 581 L 1.000** 3.499 +- 0.042 584 N 1.000** 3.499 +- 0.032 614 S 1.000** 3.499 +- 0.042 661 L 1.000** 3.499 +- 0.036 663 T 0.997** 3.492 +- 0.133 686 G 1.000** 3.498 +- 0.063 696 V 0.575 2.403 +- 1.274 728 I 1.000** 3.499 +- 0.033 772 V 0.999** 3.496 +- 0.096 773 F 1.000** 3.499 +- 0.036