--- 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