--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Tue Jan 23 23:07:50 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_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -46829.37 -46875.01 2 -46826.96 -46876.45 -------------------------------------- TOTAL -46827.56 -46875.97 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/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} 7.835093 0.048588 7.388076 8.258520 7.824838 522.49 825.16 1.000 r(A<->C){all} 0.145315 0.000033 0.133576 0.156111 0.145293 292.97 387.22 1.002 r(A<->G){all} 0.265284 0.000129 0.242404 0.285663 0.265236 140.54 164.14 1.001 r(A<->T){all} 0.049455 0.000008 0.043833 0.054798 0.049446 496.19 531.48 1.001 r(C<->G){all} 0.072205 0.000027 0.062387 0.082184 0.072172 564.30 571.35 1.000 r(C<->T){all} 0.383739 0.000164 0.358880 0.407808 0.383664 156.16 170.13 1.002 r(G<->T){all} 0.084002 0.000021 0.075477 0.093131 0.083938 330.98 390.68 1.000 pi(A){all} 0.400853 0.000044 0.386580 0.412449 0.400805 448.81 451.16 1.000 pi(C){all} 0.155870 0.000023 0.146719 0.165009 0.155762 260.32 329.84 1.000 pi(G){all} 0.230024 0.000044 0.216906 0.242461 0.230151 151.41 191.22 1.000 pi(T){all} 0.213254 0.000038 0.200874 0.224933 0.213144 303.53 310.06 1.000 alpha{1,2} 0.455799 0.000507 0.412984 0.500649 0.454861 671.52 726.63 1.001 alpha{3} 1.000879 0.003938 0.879968 1.121255 0.997946 982.20 1080.37 1.000 pinvar{all} 0.182920 0.000234 0.151893 0.211025 0.182903 889.89 898.39 1.002 ------------------------------------------------------------------------------------------------------ * 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 -39499.780509 Model 2: PositiveSelection -38800.288381 Model 0: one-ratio -42177.068401 Model 3: discrete -38772.241635 Model 7: beta -39306.355662 Model 8: beta&w>1 -38679.867436 Model 0 vs 1 5354.575784000001 Model 2 vs 1 1398.984255999996 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.CAP327.2.00_C6.37.KF114885_) Pr(w>1) post mean +- SE for w 7 L 1.000** 3.633 10 W 1.000** 3.633 12 Q 0.990** 3.607 24 N 0.566 2.490 76 V 1.000** 3.633 122 T 1.000** 3.633 124 A 1.000** 3.633 125 N 1.000** 3.633 126 L 1.000** 3.633 127 K 1.000** 3.633 128 E 1.000** 3.633 141 Q 1.000** 3.633 143 Y 0.776 3.043 153 P 0.883 3.325 155 N 0.999** 3.630 156 Y 1.000** 3.633 157 S 1.000** 3.633 158 E 1.000** 3.633 177 T 0.990** 3.608 208 H 0.994** 3.617 245 L 0.928 3.445 247 D 0.703 2.852 249 A 0.980* 3.582 259 S 0.946 3.490 261 E 0.977* 3.573 268 D 1.000** 3.633 286 N 0.999** 3.632 300 K 0.998** 3.628 301 G 1.000** 3.633 305 T 0.983* 3.589 308 K 1.000** 3.633 309 R 1.000** 3.633 311 E 0.979* 3.579 312 K 1.000** 3.633 315 K 0.999** 3.631 322 N 1.000** 3.633 324 A 1.000** 3.633 325 P 1.000** 3.633 326 P 1.000** 3.633 351 E 1.000** 3.633 355 T 0.665 2.752 356 S 1.000** 3.633 357 E 1.000** 3.633 358 L 1.000** 3.633 360 K 1.000** 3.633 361 T 0.999** 3.632 377 E 0.985* 3.593 388 A 1.000** 3.633 394 V 1.000** 3.633 408 N 1.000** 3.633 409 N 1.000** 3.633 410 N 1.000** 3.633 411 N 1.000** 3.633 412 N 1.000** 3.633 447 Q 1.000** 3.633 553 N 1.000** 3.633 558 S 0.999** 3.632 565 D 1.000** 3.633 568 D 1.000** 3.633 584 D 1.000** 3.633 588 K 1.000** 3.633 618 D 1.000** 3.633 665 I 1.000** 3.633 667 N 0.767 3.020 668 P 0.996** 3.623 687 N 0.920 3.422 690 I 1.000** 3.633 691 R 0.585 2.539 694 N 0.981* 3.583 700 A 0.988* 3.602 714 Q 0.999** 3.630 732 A 1.000** 3.633 776 I 1.000** 3.633 777 C 1.000** 3.633 781 L 1.000** 3.633 791 F 0.639 2.683 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.CAP327.2.00_C6.37.KF114885_) Pr(w>1) post mean +- SE for w 7 L 1.000** 3.499 +- 0.038 10 W 1.000** 3.500 +- 0.000 12 Q 0.991** 3.479 +- 0.231 24 N 0.659 2.647 +- 1.185 76 V 1.000** 3.500 +- 0.005 122 T 1.000** 3.500 +- 0.017 124 A 1.000** 3.500 +- 0.000 125 N 1.000** 3.500 +- 0.000 126 L 1.000** 3.500 +- 0.000 127 K 1.000** 3.500 +- 0.000 128 E 1.000** 3.499 +- 0.041 141 Q 1.000** 3.500 +- 0.011 143 Y 0.823 3.058 +- 0.954 153 P 0.913 3.283 +- 0.704 155 N 0.999** 3.497 +- 0.087 156 Y 1.000** 3.500 +- 0.000 157 S 1.000** 3.500 +- 0.001 158 E 1.000** 3.500 +- 0.000 177 T 0.991** 3.477 +- 0.237 208 H 0.995** 3.487 +- 0.182 245 L 0.937 3.343 +- 0.606 247 D 0.776 2.939 +- 1.043 249 A 0.984* 3.460 +- 0.315 259 S 0.955* 3.387 +- 0.519 261 E 0.984* 3.460 +- 0.315 268 D 1.000** 3.500 +- 0.004 286 N 1.000** 3.499 +- 0.051 300 K 0.999** 3.496 +- 0.096 301 G 1.000** 3.500 +- 0.000 305 T 0.987* 3.468 +- 0.281 308 K 1.000** 3.500 +- 0.014 309 R 1.000** 3.500 +- 0.028 311 E 0.983* 3.458 +- 0.320 312 K 1.000** 3.500 +- 0.004 315 K 0.999** 3.498 +- 0.070 322 N 1.000** 3.500 +- 0.001 324 A 1.000** 3.500 +- 0.003 325 P 1.000** 3.500 +- 0.003 326 P 1.000** 3.499 +- 0.038 351 E 1.000** 3.500 +- 0.001 355 T 0.754 2.886 +- 1.076 356 S 1.000** 3.500 +- 0.000 357 E 1.000** 3.500 +- 0.000 358 L 1.000** 3.500 +- 0.000 360 K 1.000** 3.500 +- 0.000 361 T 0.999** 3.499 +- 0.056 377 E 0.989* 3.471 +- 0.266 388 A 1.000** 3.500 +- 0.017 394 V 1.000** 3.500 +- 0.002 408 N 1.000** 3.500 +- 0.000 409 N 1.000** 3.500 +- 0.000 410 N 1.000** 3.500 +- 0.000 411 N 1.000** 3.500 +- 0.000 412 N 1.000** 3.500 +- 0.002 447 Q 1.000** 3.500 +- 0.024 534 K 0.506 2.265 +- 1.250 553 N 1.000** 3.500 +- 0.000 558 S 0.999** 3.499 +- 0.058 565 D 1.000** 3.500 +- 0.000 568 D 1.000** 3.500 +- 0.003 584 D 1.000** 3.500 +- 0.000 588 K 1.000** 3.499 +- 0.041 618 D 1.000** 3.500 +- 0.000 665 I 1.000** 3.500 +- 0.015 667 N 0.817 3.044 +- 0.966 668 P 0.996** 3.491 +- 0.154 687 N 0.939 3.349 +- 0.596 690 I 1.000** 3.500 +- 0.012 691 R 0.626 2.566 +- 1.209 694 N 0.985* 3.463 +- 0.302 700 A 0.989* 3.474 +- 0.256 714 Q 0.999** 3.497 +- 0.090 732 A 1.000** 3.500 +- 0.015 776 I 1.000** 3.500 +- 0.033 777 C 1.000** 3.500 +- 0.000 781 L 1.000** 3.500 +- 0.005 791 F 0.698 2.746 +- 1.148 Model 8 vs 7 1252.9764520000026 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.CAP327.2.00_C6.37.KF114885_) Pr(w>1) post mean +- SE for w 7 L 1.000** 3.159 10 W 1.000** 3.160 12 Q 0.989* 3.136 24 N 0.595 2.264 76 V 1.000** 3.159 122 T 1.000** 3.159 124 A 1.000** 3.160 125 N 1.000** 3.160 126 L 1.000** 3.160 127 K 1.000** 3.160 128 E 0.999** 3.158 141 Q 1.000** 3.159 143 Y 0.805 2.726 153 P 0.892 2.922 155 N 0.998** 3.154 156 Y 1.000** 3.160 157 S 1.000** 3.160 158 E 1.000** 3.160 177 T 0.991** 3.140 208 H 0.993** 3.143 245 L 0.933 3.011 247 D 0.709 2.518 249 A 0.983* 3.122 259 S 0.954* 3.058 261 E 0.972* 3.097 268 D 1.000** 3.160 286 N 0.999** 3.158 300 K 0.997** 3.153 301 G 1.000** 3.160 305 T 0.980* 3.114 308 K 1.000** 3.159 309 R 1.000** 3.159 311 E 0.979* 3.113 312 K 1.000** 3.159 315 K 0.998** 3.156 322 N 1.000** 3.160 324 A 1.000** 3.160 325 P 1.000** 3.160 326 P 1.000** 3.159 351 E 1.000** 3.160 355 T 0.671 2.433 356 S 1.000** 3.160 357 E 1.000** 3.160 358 L 1.000** 3.160 360 K 1.000** 3.160 361 T 0.999** 3.158 377 E 0.983* 3.122 388 A 1.000** 3.159 394 V 1.000** 3.160 408 N 1.000** 3.160 409 N 1.000** 3.160 410 N 1.000** 3.160 411 N 1.000** 3.160 412 N 1.000** 3.160 447 Q 1.000** 3.159 553 N 1.000** 3.160 558 S 0.999** 3.158 565 D 1.000** 3.160 568 D 1.000** 3.160 584 D 1.000** 3.160 588 K 1.000** 3.159 618 D 1.000** 3.160 665 I 1.000** 3.159 667 N 0.800 2.718 668 P 0.996** 3.151 687 N 0.925 2.994 690 I 1.000** 3.159 691 R 0.582 2.222 694 N 0.978* 3.111 700 A 0.989* 3.135 714 Q 0.999** 3.156 732 A 1.000** 3.159 776 I 1.000** 3.159 777 C 1.000** 3.160 781 L 1.000** 3.160 791 F 0.614 2.296 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.CAP327.2.00_C6.37.KF114885_) Pr(w>1) post mean +- SE for w 7 L 0.999** 3.498 +- 0.070 10 W 1.000** 3.500 +- 0.001 12 Q 0.962* 3.404 +- 0.487 76 V 1.000** 3.500 +- 0.010 122 T 1.000** 3.499 +- 0.039 124 A 1.000** 3.500 +- 0.000 125 N 1.000** 3.500 +- 0.000 126 L 1.000** 3.500 +- 0.000 127 K 1.000** 3.500 +- 0.000 128 E 0.998** 3.494 +- 0.120 141 Q 1.000** 3.500 +- 0.016 153 P 0.598 2.471 +- 1.255 155 N 0.990** 3.475 +- 0.251 156 Y 1.000** 3.500 +- 0.000 157 S 1.000** 3.500 +- 0.003 158 E 1.000** 3.500 +- 0.000 177 T 0.976* 3.438 +- 0.394 208 H 0.974* 3.433 +- 0.407 245 L 0.805 3.000 +- 1.016 249 A 0.934 3.331 +- 0.635 259 S 0.842 3.094 +- 0.936 261 E 0.853 3.124 +- 0.905 268 D 1.000** 3.500 +- 0.007 286 N 0.997** 3.492 +- 0.141 300 K 0.987* 3.466 +- 0.292 301 G 1.000** 3.500 +- 0.000 305 T 0.907 3.263 +- 0.742 308 K 1.000** 3.500 +- 0.033 309 R 1.000** 3.499 +- 0.053 311 E 0.916 3.284 +- 0.711 312 K 1.000** 3.500 +- 0.010 315 K 0.994** 3.484 +- 0.198 322 N 1.000** 3.500 +- 0.002 324 A 1.000** 3.500 +- 0.007 325 P 1.000** 3.500 +- 0.005 326 P 1.000** 3.499 +- 0.052 351 E 1.000** 3.500 +- 0.002 356 S 1.000** 3.500 +- 0.000 357 E 1.000** 3.500 +- 0.000 358 L 1.000** 3.500 +- 0.000 360 K 1.000** 3.500 +- 0.000 361 T 0.998** 3.494 +- 0.123 377 E 0.917 3.288 +- 0.704 388 A 1.000** 3.499 +- 0.042 394 V 1.000** 3.500 +- 0.005 408 N 1.000** 3.500 +- 0.000 409 N 1.000** 3.500 +- 0.000 410 N 1.000** 3.500 +- 0.000 411 N 1.000** 3.500 +- 0.000 412 N 1.000** 3.500 +- 0.004 447 Q 1.000** 3.499 +- 0.055 553 N 1.000** 3.500 +- 0.000 558 S 0.998** 3.496 +- 0.103 565 D 1.000** 3.500 +- 0.001 568 D 1.000** 3.500 +- 0.007 584 D 1.000** 3.500 +- 0.000 588 K 0.999** 3.497 +- 0.086 618 D 1.000** 3.500 +- 0.001 665 I 1.000** 3.500 +- 0.022 668 P 0.989* 3.473 +- 0.264 687 N 0.699 2.730 +- 1.174 690 I 1.000** 3.500 +- 0.026 694 N 0.903 3.251 +- 0.758 700 A 0.965* 3.411 +- 0.469 714 Q 0.997** 3.492 +- 0.145 732 A 1.000** 3.500 +- 0.023 776 I 0.999** 3.498 +- 0.071 777 C 1.000** 3.500 +- 0.001 781 L 1.000** 3.500 +- 0.006