--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Jan 26 22:08:29 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_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -50178.64 -50224.08 2 -50179.17 -50220.14 -------------------------------------- TOTAL -50178.87 -50223.40 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 10.502673 0.113840 9.911662 11.254180 10.489470 540.52 564.12 1.000 r(A<->C){all} 0.141198 0.000028 0.130787 0.151783 0.141111 350.49 481.77 1.002 r(A<->G){all} 0.289300 0.000094 0.271531 0.309303 0.289369 222.86 264.27 1.000 r(A<->T){all} 0.060100 0.000011 0.053249 0.065929 0.060004 518.94 535.03 1.000 r(C<->G){all} 0.075266 0.000026 0.065774 0.085408 0.075119 332.14 416.09 1.000 r(C<->T){all} 0.345880 0.000115 0.326707 0.368560 0.345459 217.80 246.73 1.000 r(G<->T){all} 0.088255 0.000021 0.079731 0.097180 0.088078 566.48 611.17 1.000 pi(A){all} 0.382923 0.000039 0.370105 0.394352 0.382881 331.65 382.85 1.000 pi(C){all} 0.172784 0.000023 0.162919 0.181803 0.172567 326.70 353.17 1.000 pi(G){all} 0.223296 0.000024 0.214625 0.233386 0.223227 295.07 330.66 1.000 pi(T){all} 0.220997 0.000031 0.210570 0.231729 0.221041 303.92 340.84 1.000 alpha{1,2} 0.446200 0.000386 0.408614 0.486364 0.445813 1015.32 1069.44 1.000 alpha{3} 1.031890 0.003635 0.918539 1.150164 1.031327 1105.13 1182.38 1.000 pinvar{all} 0.095988 0.000176 0.069434 0.120952 0.095957 979.26 993.45 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 -40904.63629 Model 2: PositiveSelection -40275.298151 Model 0: one-ratio -43299.134088 Model 3: discrete -40230.339606 Model 7: beta -40738.792083 Model 8: beta&w>1 -40146.38401 Model 0 vs 1 4788.995595999993 Model 2 vs 1 1258.676277999999 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.BW.96.96BW11B01.AF110971_) Pr(w>1) post mean +- SE for w 18 G 0.587 2.468 51 V 0.729 2.824 71 V 1.000** 3.503 118 N 0.999** 3.500 119 T 1.000** 3.503 120 V 1.000** 3.503 121 N 1.000** 3.503 122 D 1.000** 3.503 123 T 1.000** 3.503 124 L 1.000** 3.503 125 H 1.000** 3.503 134 V 0.978* 3.447 140 R 0.804 3.013 142 Y 0.918 3.296 148 L 0.915 3.290 152 P 0.925 3.316 154 N 1.000** 3.503 155 N 1.000** 3.503 156 K 1.000** 3.503 157 E 1.000** 3.503 174 S 0.995** 3.490 203 N 1.000** 3.503 240 I 0.718 2.797 252 E 0.794 2.988 255 E 0.998** 3.499 262 N 0.872 3.182 270 R 1.000** 3.503 280 A 0.998** 3.498 294 E 1.000** 3.503 295 S 1.000** 3.503 296 Q 1.000** 3.503 299 N 0.980* 3.452 302 Q 1.000** 3.503 303 R 1.000** 3.503 305 S 1.000** 3.503 306 E 1.000** 3.503 309 K 0.864 3.162 311 H 0.929 3.324 317 K 1.000** 3.503 319 N 1.000** 3.502 320 Q 1.000** 3.503 321 P 1.000** 3.503 345 K 1.000** 3.503 346 Y 1.000** 3.503 347 I 1.000** 3.503 348 T 1.000** 3.503 375 A 1.000** 3.503 377 N 1.000** 3.503 381 K 1.000** 3.503 394 K 1.000** 3.503 395 N 1.000** 3.503 396 D 1.000** 3.503 428 K 0.997** 3.496 532 A 1.000** 3.502 537 A 0.983* 3.460 544 Q 1.000** 3.503 545 E 1.000** 3.503 546 E 0.999** 3.501 549 G 1.000** 3.503 565 D 1.000** 3.503 566 T 1.000** 3.503 569 R 1.000** 3.503 573 V 0.989* 3.476 599 D 1.000** 3.503 646 T 1.000** 3.503 648 N 0.696 2.743 649 P 0.533 2.335 671 I 1.000** 3.503 672 R 0.970* 3.427 675 S 0.645 2.614 681 A 1.000** 3.503 705 R 0.775 2.940 710 I 0.999** 3.500 719 Q 0.943 3.359 750 L 0.529 2.324 751 I 0.980* 3.453 754 I 0.997** 3.496 755 G 0.998** 3.497 759 R 0.733 2.834 769 F 0.995** 3.491 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.BW.96.96BW11B01.AF110971_) Pr(w>1) post mean +- SE for w 18 G 0.678 2.695 +- 1.168 51 V 0.797 2.994 +- 1.005 71 V 1.000** 3.500 +- 0.001 118 N 0.999** 3.498 +- 0.071 119 T 1.000** 3.500 +- 0.013 120 V 1.000** 3.500 +- 0.000 121 N 1.000** 3.500 +- 0.000 122 D 1.000** 3.500 +- 0.001 123 T 1.000** 3.500 +- 0.000 124 L 1.000** 3.500 +- 0.000 125 H 1.000** 3.500 +- 0.000 134 V 0.984* 3.461 +- 0.309 140 R 0.857 3.142 +- 0.876 142 Y 0.941 3.353 +- 0.587 148 L 0.940 3.349 +- 0.596 152 P 0.947 3.368 +- 0.559 154 N 1.000** 3.500 +- 0.015 155 N 1.000** 3.500 +- 0.000 156 K 1.000** 3.500 +- 0.000 157 E 1.000** 3.500 +- 0.000 174 S 0.996** 3.491 +- 0.149 203 N 1.000** 3.500 +- 0.015 240 I 0.788 2.971 +- 1.021 252 E 0.849 3.123 +- 0.894 255 E 0.999** 3.497 +- 0.085 262 N 0.908 3.270 +- 0.723 270 R 1.000** 3.500 +- 0.002 280 A 0.999** 3.497 +- 0.089 294 E 1.000** 3.500 +- 0.001 295 S 1.000** 3.500 +- 0.000 296 Q 1.000** 3.500 +- 0.001 299 N 0.986* 3.464 +- 0.296 302 Q 1.000** 3.500 +- 0.002 303 R 1.000** 3.500 +- 0.000 305 S 1.000** 3.500 +- 0.000 306 E 1.000** 3.500 +- 0.000 309 K 0.902 3.255 +- 0.743 311 H 0.949 3.374 +- 0.548 317 K 1.000** 3.500 +- 0.000 319 N 1.000** 3.499 +- 0.039 320 Q 1.000** 3.500 +- 0.000 321 P 1.000** 3.500 +- 0.003 345 K 1.000** 3.500 +- 0.000 346 Y 1.000** 3.500 +- 0.001 347 I 1.000** 3.500 +- 0.000 348 T 1.000** 3.500 +- 0.003 375 A 1.000** 3.500 +- 0.003 377 N 1.000** 3.500 +- 0.000 381 K 1.000** 3.500 +- 0.006 394 K 1.000** 3.500 +- 0.000 395 N 1.000** 3.500 +- 0.000 396 D 1.000** 3.500 +- 0.000 428 K 0.998** 3.495 +- 0.106 532 A 1.000** 3.500 +- 0.024 537 A 0.988* 3.470 +- 0.271 544 Q 1.000** 3.500 +- 0.000 545 E 1.000** 3.500 +- 0.004 546 E 1.000** 3.499 +- 0.051 549 G 1.000** 3.500 +- 0.004 565 D 1.000** 3.500 +- 0.000 566 T 1.000** 3.500 +- 0.015 569 R 1.000** 3.500 +- 0.000 573 V 0.993** 3.481 +- 0.216 599 D 1.000** 3.500 +- 0.004 646 T 1.000** 3.500 +- 0.013 648 N 0.771 2.927 +- 1.051 649 P 0.629 2.572 +- 1.208 671 I 1.000** 3.500 +- 0.003 672 R 0.979* 3.446 +- 0.362 675 S 0.728 2.820 +- 1.112 681 A 1.000** 3.500 +- 0.004 705 R 0.834 3.085 +- 0.930 710 I 0.999** 3.498 +- 0.072 719 Q 0.959* 3.398 +- 0.494 750 L 0.625 2.563 +- 1.210 751 I 0.986* 3.465 +- 0.293 754 I 0.998** 3.495 +- 0.110 755 G 0.998** 3.496 +- 0.099 759 R 0.800 3.001 +- 0.999 769 F 0.997** 3.492 +- 0.142 Model 8 vs 7 1184.8161459999974 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.BW.96.96BW11B01.AF110971_) Pr(w>1) post mean +- SE for w 18 G 0.819 2.598 51 V 0.879 2.721 71 V 1.000** 2.973 118 N 0.999** 2.971 119 T 1.000** 2.972 120 V 1.000** 2.973 121 N 1.000** 2.973 122 D 1.000** 2.973 123 T 1.000** 2.973 124 L 1.000** 2.973 125 H 1.000** 2.973 134 V 0.991** 2.954 140 R 0.913 2.792 142 Y 0.965* 2.901 148 L 0.960* 2.891 152 P 0.969* 2.909 154 N 1.000** 2.972 155 N 1.000** 2.973 156 K 1.000** 2.973 157 E 1.000** 2.973 174 S 0.998** 2.968 203 N 1.000** 2.972 240 I 0.853 2.665 252 E 0.918 2.803 253 S 0.608 2.152 255 E 0.999** 2.971 262 N 0.940 2.848 270 R 1.000** 2.973 280 A 0.999** 2.971 294 E 1.000** 2.973 295 S 1.000** 2.973 296 Q 1.000** 2.973 299 N 0.991** 2.954 302 Q 1.000** 2.973 303 R 1.000** 2.973 305 S 1.000** 2.973 306 E 1.000** 2.973 309 K 0.943 2.854 311 H 0.965* 2.901 317 K 1.000** 2.973 319 N 1.000** 2.972 320 Q 1.000** 2.973 321 P 1.000** 2.973 345 K 1.000** 2.973 346 Y 1.000** 2.973 347 I 1.000** 2.973 348 T 1.000** 2.973 375 A 1.000** 2.973 377 N 1.000** 2.973 381 K 1.000** 2.972 394 K 1.000** 2.973 395 N 1.000** 2.973 396 D 1.000** 2.973 428 K 0.999** 2.970 532 A 1.000** 2.972 537 A 0.992** 2.956 544 Q 1.000** 2.973 545 E 1.000** 2.973 546 E 1.000** 2.972 549 G 1.000** 2.973 565 D 1.000** 2.973 566 T 1.000** 2.972 569 R 1.000** 2.973 573 V 0.996** 2.963 599 D 1.000** 2.973 602 K 0.509 1.956 646 T 1.000** 2.972 648 N 0.856 2.673 649 P 0.733 2.413 671 I 1.000** 2.973 672 R 0.971* 2.913 675 S 0.829 2.620 681 A 1.000** 2.973 705 R 0.885 2.733 710 I 0.999** 2.971 719 Q 0.966* 2.902 750 L 0.754 2.464 751 I 0.992** 2.955 754 I 0.999** 2.970 755 G 0.999** 2.970 759 R 0.864 2.689 769 F 0.996** 2.965 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.BW.96.96BW11B01.AF110971_) Pr(w>1) post mean +- SE for w 18 G 0.753 2.224 +- 0.805 48 E 0.542 1.790 +- 0.812 51 V 0.827 2.411 +- 0.778 71 V 1.000** 2.836 +- 0.472 118 N 0.999** 2.832 +- 0.477 119 T 1.000** 2.836 +- 0.472 120 V 1.000** 2.836 +- 0.472 121 N 1.000** 2.836 +- 0.472 122 D 1.000** 2.836 +- 0.472 123 T 1.000** 2.836 +- 0.472 124 L 1.000** 2.836 +- 0.472 125 H 1.000** 2.836 +- 0.472 134 V 0.971* 2.762 +- 0.558 140 R 0.866 2.507 +- 0.741 142 Y 0.953* 2.723 +- 0.605 148 L 0.940 2.691 +- 0.630 152 P 0.946 2.703 +- 0.617 154 N 1.000** 2.836 +- 0.472 155 N 1.000** 2.836 +- 0.472 156 K 1.000** 2.836 +- 0.472 157 E 1.000** 2.836 +- 0.472 174 S 0.997** 2.830 +- 0.482 203 N 1.000** 2.836 +- 0.472 240 I 0.847 2.478 +- 0.782 244 A 0.533 1.786 +- 0.851 252 E 0.853 2.469 +- 0.750 253 S 0.664 2.061 +- 0.881 255 E 0.998** 2.832 +- 0.477 262 N 0.908 2.610 +- 0.688 270 R 1.000** 2.836 +- 0.472 280 A 0.999** 2.833 +- 0.477 287 E 0.605 1.913 +- 0.832 294 E 1.000** 2.836 +- 0.472 295 S 1.000** 2.836 +- 0.472 296 Q 1.000** 2.836 +- 0.472 299 N 0.982* 2.791 +- 0.529 302 Q 1.000** 2.836 +- 0.472 303 R 1.000** 2.836 +- 0.472 305 S 1.000** 2.836 +- 0.472 306 E 1.000** 2.836 +- 0.472 309 K 0.896 2.579 +- 0.701 311 H 0.952* 2.720 +- 0.607 317 K 1.000** 2.836 +- 0.472 319 N 1.000** 2.835 +- 0.473 320 Q 1.000** 2.836 +- 0.472 321 P 1.000** 2.836 +- 0.472 345 K 1.000** 2.836 +- 0.472 346 Y 1.000** 2.836 +- 0.472 347 I 1.000** 2.836 +- 0.472 348 T 1.000** 2.836 +- 0.472 375 A 1.000** 2.836 +- 0.472 377 N 1.000** 2.836 +- 0.472 381 K 1.000** 2.836 +- 0.472 394 K 1.000** 2.836 +- 0.472 395 N 1.000** 2.836 +- 0.472 396 D 1.000** 2.836 +- 0.472 428 K 0.998** 2.831 +- 0.480 532 A 1.000** 2.836 +- 0.473 537 A 0.990* 2.812 +- 0.506 544 Q 1.000** 2.836 +- 0.472 545 E 1.000** 2.836 +- 0.472 546 E 0.999** 2.835 +- 0.474 549 G 1.000** 2.836 +- 0.472 561 S 0.505 1.725 +- 0.809 565 D 1.000** 2.836 +- 0.472 566 T 1.000** 2.836 +- 0.472 569 R 1.000** 2.836 +- 0.472 573 V 0.989* 2.809 +- 0.507 599 D 1.000** 2.836 +- 0.472 602 K 0.617 1.932 +- 0.820 646 T 1.000** 2.836 +- 0.472 648 N 0.829 2.425 +- 0.788 649 P 0.757 2.276 +- 0.863 671 I 1.000** 2.836 +- 0.472 672 R 0.974* 2.781 +- 0.559 675 S 0.772 2.275 +- 0.806 681 A 1.000** 2.836 +- 0.472 695 R 0.556 1.842 +- 0.886 705 R 0.881 2.560 +- 0.742 710 I 0.999** 2.834 +- 0.475 719 Q 0.962* 2.748 +- 0.586 733 L 0.536 1.793 +- 0.868 750 L 0.737 2.199 +- 0.825 751 I 0.984* 2.797 +- 0.522 754 I 0.998** 2.831 +- 0.479 755 G 0.999** 2.833 +- 0.477 759 R 0.857 2.499 +- 0.770 769 F 0.996** 2.827 +- 0.486