--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 16:37:27 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=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=
tcoffee.dir=
tcoffee.minScore=3
input.fasta=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-B/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       -4171.12          -4188.03
2       -4171.16          -4187.07
--------------------------------------
TOTAL     -4171.14          -4187.66
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-B/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}           0.627749      0.001702      0.550000      0.712000      0.626000      1.001
r(A<->C){all}     0.134005      0.000360      0.098782      0.172906      0.133211      1.003
r(A<->G){all}     0.284803      0.000745      0.234453      0.340036      0.284435      1.000
r(A<->T){all}     0.154298      0.000751      0.103732      0.210782      0.153062      1.000
r(C<->G){all}     0.100612      0.000168      0.076849      0.127632      0.100068      1.000
r(C<->T){all}     0.219640      0.000647      0.172784      0.272735      0.218589      1.001
r(G<->T){all}     0.106642      0.000313      0.073956      0.143659      0.105904      1.000
pi(A){all}        0.191798      0.000101      0.172470      0.212256      0.191536      1.001
pi(C){all}        0.301237      0.000141      0.278043      0.324580      0.301377      1.000
pi(G){all}        0.336693      0.000151      0.312950      0.361432      0.336605      1.000
pi(T){all}        0.170273      0.000096      0.151698      0.189763      0.170126      1.000
alpha{1,2}        0.598254      0.025826      0.360302      0.978416      0.573430      1.000
alpha{3}         90.738893   3641.074553      3.122157    194.189996     87.289994      1.001
pinvar{all}       0.381108      0.003557      0.250192      0.484477      0.385870      1.001
---------------------------------------------------------------------------------------------
* 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	-3732.040354
Model 7: beta	-3775.537668
Model 1: NearlyNeutral	-3766.262518
Model 2: PositiveSelection	-3732.126421


Model 2 vs 1	68.27219400000013

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_005505.2_HLA-B)

            Pr(w>1)     post mean +- SE for w

    30 Y      0.978*        4.153
    32 S      0.534         2.722
    45 S      0.863         3.782
    66 E      0.935         4.015
    73 I      0.935         4.017
    84 N      0.948         4.056
    87 I      0.978*        4.155
    88 Y      0.962*        4.104
    90 A      0.725         3.339
    91 Q      0.987*        4.184
    92 A      0.591         2.878
    95 D      0.970*        4.127
    98 S      0.797         3.572
   101 N      0.580         2.871
   116 L      0.874         3.818
   118 S      0.933         4.011
   135 D      1.000**       4.224
   137 Y      0.584         2.883
   173 E      0.997**       4.214
   177 R      0.999**       4.223
   184 E      1.000**       4.224
   257 A      0.627         2.998
   325 S      0.711         3.277
   333 S      0.614         2.953
   337 C      0.997**       4.216
   340 S      0.688         3.216
   341 A      0.591         2.906
   344 S      0.590         2.875
   347 S      0.627         2.996
   350 A      0.960*        4.098

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_005505.2_HLA-B)

            Pr(w>1)     post mean +- SE for w

    30 Y      0.979*        4.068 +- 0.824
    32 S      0.596         2.770 +- 1.546
    45 S      0.876         3.716 +- 1.210
    66 E      0.938         3.923 +- 1.005
    73 I      0.943         3.948 +- 0.993
    84 N      0.953*        3.978 +- 0.950
    87 I      0.980*        4.074 +- 0.818
    88 Y      0.966*        4.024 +- 0.891
    90 A      0.759         3.316 +- 1.430
    91 Q      0.988*        4.100 +- 0.774
    92 A      0.631         2.872 +- 1.620
    95 D      0.972*        4.045 +- 0.860
    97 E      0.519         2.507 +- 1.522
    98 S      0.818         3.507 +- 1.330
   101 N      0.634         2.880 +- 1.514
   116 L      0.885         3.740 +- 1.182
   118 S      0.939         3.930 +- 1.005
   135 D      1.000**       4.138 +- 0.704
   137 Y      0.635         2.886 +- 1.519
   173 E      0.997**       4.130 +- 0.721
   177 R      0.999**       4.137 +- 0.706
   184 E      1.000**       4.138 +- 0.703
   257 A      0.663         2.986 +- 1.600
   325 S      0.740         3.254 +- 1.523
   333 S      0.651         2.942 +- 1.607
   335 A      0.541         2.559 +- 1.634
   337 C      0.997**       4.130 +- 0.719
   340 S      0.724         3.199 +- 1.489
   341 A      0.641         2.898 +- 1.510
   344 S      0.630         2.868 +- 1.619
   347 S      0.663         2.983 +- 1.599
   350 A      0.965*        4.026 +- 0.898


Model 8 vs 7	86.99462799999947

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_005505.2_HLA-B)

            Pr(w>1)     post mean +- SE for w

    30 Y      0.996**       3.827
    32 S      0.749         3.054
    45 S      0.947         3.674
    66 E      0.986*        3.796
    73 I      0.982*        3.785
    84 N      0.989*        3.806
    87 I      0.996**       3.826
    88 Y      0.991**       3.813
    90 A      0.897         3.520
    91 Q      0.998**       3.833
    92 A      0.702         2.883
    95 D      0.993**       3.819
    97 E      0.698         2.897
    98 S      0.943         3.664
   101 N      0.830         3.312
   116 L      0.961*        3.719
   118 S      0.984*        3.791
   124 V      0.662         2.782
   135 D      1.000**       3.839
   137 Y      0.806         3.233
   142 K      0.604         2.601
   152 R      0.605         2.601
   173 E      0.999**       3.838
   177 R      1.000**       3.839
   184 E      1.000**       3.839
   257 A      0.732         2.980
   325 S      0.800         3.200
   333 S      0.722         2.947
   335 A      0.614         2.599
   337 C      0.999**       3.838
   340 S      0.829         3.302
   341 A      0.824         3.292
   344 S      0.702         2.883
   347 S      0.733         2.984
   350 A      0.986*        3.795

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_005505.2_HLA-B)

            Pr(w>1)     post mean +- SE for w

    30 Y      0.996**       3.579 +- 0.394
    32 S      0.829         3.077 +- 1.109
    45 S      0.962*        3.474 +- 0.644
    66 E      0.989*        3.556 +- 0.457
    73 I      0.986*        3.549 +- 0.480
    84 N      0.991**       3.563 +- 0.439
    87 I      0.996**       3.579 +- 0.395
    88 Y      0.993**       3.569 +- 0.425
    90 A      0.928         3.375 +- 0.794
    91 Q      0.998**       3.584 +- 0.380
    92 A      0.781         2.927 +- 1.255
    95 D      0.994**       3.573 +- 0.413
    97 E      0.798         2.985 +- 1.166
    98 S      0.959*        3.466 +- 0.645
   101 N      0.886         3.246 +- 0.939
   111 A      0.560         2.272 +- 1.458
   116 L      0.972*        3.504 +- 0.580
   118 S      0.988*        3.553 +- 0.467
   124 V      0.772         2.907 +- 1.219
   134 H      0.535         2.176 +- 1.497
   135 D      1.000**       3.589 +- 0.362
   137 Y      0.869         3.194 +- 1.000
   142 K      0.738         2.804 +- 1.263
   152 R      0.732         2.789 +- 1.280
   173 E      0.999**       3.587 +- 0.367
   177 R      1.000**       3.589 +- 0.363
   184 E      1.000**       3.589 +- 0.362
   188 W      0.556         2.258 +- 1.446
   257 A      0.804         2.995 +- 1.211
   325 S      0.853         3.146 +- 1.092
   333 S      0.796         2.972 +- 1.225
   335 A      0.716         2.725 +- 1.360
   337 C      0.999**       3.588 +- 0.366
   340 S      0.880         3.229 +- 0.986
   341 A      0.882         3.231 +- 0.957
   344 S      0.782         2.927 +- 1.255
   347 S      0.805         2.998 +- 1.208
   350 A      0.989*        3.557 +- 0.465