--- 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
