--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Apr 12 01:18:33 WEST 2018 codeml.models=1 2 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir=/home/jorge/Data/ADOPS/paml4.5/bin/ input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir=/home/jorge/Data/ADOPS/mrbayes-3.1.2 tcoffee.dir= tcoffee.minScore=3 input.fasta=/home/jorge/Data/ADOPS/HLA/HLA-F/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-F/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-F/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -3019.67 -3029.87 2 -3019.65 -3029.13 -------------------------------------- TOTAL -3019.66 -3029.57 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-F/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-F/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Summaries are based on a total of 15002 samples from 2 runs) (Each run produced 10001 samples of which 7501 samples were included) 95% Cred. Interval ---------------------- Parameter Mean Variance Lower Upper Median PSRF * --------------------------------------------------------------------------------------------- TL{all} 0.197659 0.000258 0.169000 0.231000 0.197000 1.000 r(A<->C){all} 0.081404 0.000440 0.044771 0.127338 0.079824 1.000 r(A<->G){all} 0.253176 0.000980 0.194080 0.317189 0.252338 1.000 r(A<->T){all} 0.174269 0.001101 0.114139 0.243117 0.172482 1.000 r(C<->G){all} 0.092963 0.000325 0.060665 0.131276 0.091845 1.001 r(C<->T){all} 0.301237 0.001239 0.234489 0.372372 0.300499 1.000 r(G<->T){all} 0.096950 0.000468 0.058380 0.142607 0.095840 1.000 pi(A){all} 0.204498 0.000108 0.184368 0.225420 0.204356 1.001 pi(C){all} 0.281078 0.000132 0.258681 0.303060 0.281026 1.000 pi(G){all} 0.315159 0.000146 0.291571 0.338866 0.315204 1.001 pi(T){all} 0.199265 0.000103 0.179598 0.219472 0.199220 1.000 alpha{1,2} 84.384989 3958.226981 0.432626 193.771056 80.074272 1.000 alpha{3} 105.607470 3032.582631 10.558309 195.163974 107.133730 1.000 pinvar{all} 0.426555 0.016495 0.114577 0.620409 0.448777 1.002 --------------------------------------------------------------------------------------------- * Convergence diagnostic (PSRF = Potential scale reduction factor [Gelman and Rubin, 1992], uncorrected) should approach 1 as runs converge. The values may be unreliable if you have a small number of samples. PSRF should only be used as a rough guide to convergence since all the assumptions that allow one to interpret it as a scale reduction factor are not met in the phylogenetic context. --- CODEML SUMMARY Model 8: beta&w>1 -2765.486949 Model 7: beta -2776.266145 Model 1: NearlyNeutral -2776.180405 Model 2: PositiveSelection -2765.481998 Model 2 vs 1 21.396813999999722 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_001091949.1_HLA-F) Pr(w>1) post mean +- SE for w 83 W 0.822 2.883 210 V 0.769 2.704 218 H 0.641 2.269 272 P 0.659 2.328 281 H 0.633 2.242 297 Q 0.970* 3.382 313 V 0.681 2.403 316 G 0.991** 3.454 317 A 0.680 2.402 344 A 0.701 2.472 345 A 0.733 2.579 346 A 1.000** 3.485 347 Y 0.999** 3.482 348 S 0.996** 3.473 349 V 0.793 2.783 350 V 0.961* 3.353 352 G 0.740 2.604 357 T 0.984* 3.432 360 S 0.779 2.736 373 L 0.706 2.489 380 S 0.641 2.269 388 G 0.992** 3.459 389 D 0.970* 3.384 390 M 0.950 3.314 391 W 0.974* 3.396 393 T 0.762 2.680 394 S 0.988* 3.446 396 N 0.952* 3.321 398 A 0.999** 3.482 402 L 0.990* 3.451 403 Q 0.644 2.278 404 S 0.997** 3.474 405 L 0.699 2.466 406 R 0.965* 3.367 407 F 0.999** 3.483 408 G 0.971* 3.388 409 F 0.504 1.805 411 F 0.891 3.116 412 R 0.986* 3.438 415 S 0.999** 3.481 417 L 0.990* 3.451 418 L 0.987* 3.441 419 R 1.000** 3.484 420 S 1.000** 3.484 422 H 0.999** 3.482 423 H 0.978* 3.410 424 L 0.989* 3.448 425 M 0.999** 3.481 426 K 0.981* 3.419 427 R 0.953* 3.327 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: Homo_sapiens_Hominidae_Haplorrhini_NP_001091949.1_HLA-F) Pr(w>1) post mean +- SE for w 83 W 0.612 2.601 +- 1.650 210 V 0.622 2.647 +- 1.744 272 P 0.508 2.211 +- 1.704 297 Q 0.746 3.115 +- 1.532 313 V 0.530 2.296 +- 1.720 316 G 0.890 3.668 +- 1.416 317 A 0.530 2.295 +- 1.720 344 A 0.551 2.375 +- 1.731 345 A 0.583 2.498 +- 1.741 346 A 0.978* 3.977 +- 1.214 347 Y 0.921 3.770 +- 1.343 348 S 0.945 3.872 +- 1.310 349 V 0.596 2.549 +- 1.676 350 V 0.722 3.035 +- 1.553 352 G 0.590 2.526 +- 1.741 357 T 0.836 3.460 +- 1.483 360 S 0.636 2.703 +- 1.749 373 L 0.542 2.336 +- 1.703 388 G 0.895 3.680 +- 1.403 389 D 0.751 3.138 +- 1.533 390 M 0.659 2.794 +- 1.529 391 W 0.758 3.156 +- 1.518 393 T 0.617 2.628 +- 1.749 394 S 0.868 3.583 +- 1.447 396 N 0.662 2.802 +- 1.524 398 A 0.919 3.760 +- 1.345 402 L 0.895 3.690 +- 1.413 403 Q 0.505 2.207 +- 1.726 404 S 0.868 3.557 +- 1.405 405 L 0.547 2.360 +- 1.726 406 R 0.715 2.995 +- 1.527 407 F 0.951* 3.882 +- 1.284 408 G 0.756 3.153 +- 1.530 411 F 0.761 3.174 +- 1.653 412 R 0.838 3.458 +- 1.469 415 S 0.878 3.597 +- 1.394 417 L 0.879 3.623 +- 1.431 418 L 0.853 3.525 +- 1.462 419 R 0.962* 3.923 +- 1.259 420 S 0.964* 3.932 +- 1.254 422 H 0.908 3.718 +- 1.358 423 H 0.786 3.266 +- 1.511 424 L 0.872 3.595 +- 1.440 425 M 0.888 3.633 +- 1.383 426 K 0.810 3.362 +- 1.503 427 R 0.676 2.854 +- 1.533 Model 8 vs 7 21.558391999999913 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_001091949.1_HLA-F) Pr(w>1) post mean +- SE for w 83 W 0.820 2.880 210 V 0.768 2.703 218 H 0.640 2.269 272 P 0.657 2.328 281 H 0.632 2.242 297 Q 0.967* 3.378 313 V 0.679 2.402 316 G 0.990** 3.455 317 A 0.679 2.402 344 A 0.699 2.472 345 A 0.731 2.578 346 A 1.000** 3.489 347 Y 0.999** 3.485 348 S 0.996** 3.475 349 V 0.791 2.780 350 V 0.958* 3.347 352 G 0.739 2.604 357 T 0.983* 3.431 360 S 0.777 2.736 373 L 0.704 2.488 380 S 0.640 2.269 388 G 0.991** 3.460 389 D 0.968* 3.380 390 M 0.946 3.306 391 W 0.971* 3.393 393 T 0.761 2.679 394 S 0.987* 3.446 396 N 0.948 3.313 398 A 0.999** 3.485 402 L 0.989* 3.452 403 Q 0.642 2.278 404 S 0.996** 3.477 405 L 0.698 2.466 406 R 0.962* 3.362 407 F 0.999** 3.487 408 G 0.969* 3.385 409 F 0.503 1.806 411 F 0.890 3.117 412 R 0.985* 3.438 415 S 0.998** 3.483 417 L 0.989* 3.451 418 L 0.986* 3.441 419 R 1.000** 3.488 420 S 1.000** 3.488 422 H 0.999** 3.485 423 H 0.976* 3.407 424 L 0.988* 3.449 425 M 0.998** 3.484 426 K 0.979* 3.418 427 R 0.950 3.319 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: Homo_sapiens_Hominidae_Haplorrhini_NP_001091949.1_HLA-F) Pr(w>1) post mean +- SE for w 83 W 0.767 2.830 +- 1.428 210 V 0.740 2.742 +- 1.504 218 H 0.615 2.314 +- 1.638 272 P 0.632 2.372 +- 1.626 281 H 0.607 2.289 +- 1.643 297 Q 0.900 3.282 +- 1.045 313 V 0.653 2.446 +- 1.610 316 G 0.962* 3.486 +- 0.814 317 A 0.653 2.445 +- 1.610 344 A 0.673 2.515 +- 1.591 345 A 0.704 2.620 +- 1.555 346 A 0.996** 3.590 +- 0.628 347 Y 0.982* 3.546 +- 0.705 348 S 0.982* 3.548 +- 0.716 349 V 0.743 2.751 +- 1.476 350 V 0.882 3.226 +- 1.104 352 G 0.712 2.644 +- 1.545 357 T 0.941 3.417 +- 0.904 360 S 0.751 2.778 +- 1.488 373 L 0.673 2.512 +- 1.584 380 S 0.614 2.313 +- 1.638 388 G 0.966* 3.496 +- 0.797 389 D 0.902 3.289 +- 1.041 390 M 0.852 3.123 +- 1.180 391 W 0.909 3.310 +- 1.014 393 T 0.734 2.721 +- 1.515 394 S 0.954* 3.459 +- 0.850 396 N 0.855 3.133 +- 1.170 398 A 0.982* 3.545 +- 0.706 402 L 0.962* 3.485 +- 0.820 403 Q 0.621 2.339 +- 1.639 404 S 0.968* 3.499 +- 0.769 405 L 0.671 2.507 +- 1.592 406 R 0.887 3.237 +- 1.083 407 F 0.989* 3.568 +- 0.670 408 G 0.905 3.298 +- 1.030 411 F 0.861 3.149 +- 1.233 412 R 0.945 3.427 +- 0.885 415 S 0.972* 3.514 +- 0.746 417 L 0.958* 3.473 +- 0.831 418 L 0.949 3.441 +- 0.872 419 R 0.991** 3.576 +- 0.656 420 S 0.992** 3.578 +- 0.654 422 H 0.979* 3.538 +- 0.715 423 H 0.921 3.351 +- 0.975 424 L 0.956* 3.465 +- 0.842 425 M 0.975* 3.522 +- 0.736 426 K 0.930 3.381 +- 0.944 427 R 0.861 3.154 +- 1.157