--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Apr 12 00:38:25 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-DRB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/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       -3046.22          -3074.68
2       -3046.67          -3070.64
--------------------------------------
TOTAL     -3046.42          -3074.00
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DRB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/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}           0.643768      0.002956      0.544000      0.758000      0.642000      1.000
r(A<->C){all}     0.118655      0.000467      0.079572      0.164732      0.117636      1.000
r(A<->G){all}     0.197078      0.000680      0.149119      0.251845      0.195873      1.000
r(A<->T){all}     0.210508      0.000995      0.152378      0.275912      0.209360      1.000
r(C<->G){all}     0.118134      0.000340      0.084230      0.156392      0.117161      1.000
r(C<->T){all}     0.233516      0.000985      0.176175      0.297884      0.232207      1.000
r(G<->T){all}     0.122109      0.000427      0.084644      0.165890      0.121396      1.000
pi(A){all}        0.217459      0.000182      0.191887      0.244868      0.217195      1.000
pi(C){all}        0.255244      0.000202      0.228017      0.283252      0.254923      1.000
pi(G){all}        0.323233      0.000231      0.293790      0.353179      0.323159      1.000
pi(T){all}        0.204063      0.000168      0.179256      0.230097      0.203913      1.000
alpha{1,2}        0.791847      0.139134      0.363445      1.701675      0.707111      1.001
alpha{3}          3.496540    245.027947      0.505964     12.489141      1.189538      1.000
pinvar{all}       0.511124      0.005041      0.351044      0.628224      0.519164      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	-2996.74708
Model 7: beta	-3049.409468
Model 1: NearlyNeutral	-3047.104289
Model 2: PositiveSelection	-2996.103937


Model 2 vs 1	102.00070400000004

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_002115.2_HLA-DRB1)

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

    29 S      0.662         4.319
    34 P      0.842         5.223
    38 W      0.526         3.638
    40 P      0.993**       5.978
    42 R      1.000**       6.014
    55 F      0.525         3.633
    57 D      0.990**       5.965
    61 Y      0.707         4.543
    66 S      0.999**       6.011
    76 F      0.573         3.871
    86 D      0.985*        5.937
    96 I      0.901         5.518
    99 Q      0.999**       6.009
   100 A      1.000**       6.014
   114 V      0.905         5.536
   115 V      1.000**       6.014
   133 S      0.765         4.838
   149 S      0.659         4.304
   257 S      0.981*        5.918
   258 G      0.744         4.733

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_002115.2_HLA-DRB1)

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

    29 S      0.604         4.177 +- 2.697
    34 P      0.814         5.386 +- 2.317
    40 P      0.992**       6.394 +- 1.207
    42 R      1.000**       6.439 +- 1.108
    57 D      0.984*        6.341 +- 1.286
    61 Y      0.653         4.454 +- 2.659
    66 S      0.999**       6.434 +- 1.118
    86 D      0.975*        6.285 +- 1.375
    96 I      0.845         5.493 +- 2.151
    99 Q      0.999**       6.431 +- 1.124
   100 A      1.000**       6.439 +- 1.108
   114 V      0.880         5.749 +- 2.029
   115 V      1.000**       6.439 +- 1.108
   133 S      0.723         4.864 +- 2.559
   149 S      0.596         4.119 +- 2.689
   257 S      0.978*        6.320 +- 1.352
   258 G      0.700         4.733 +- 2.602


Model 8 vs 7	105.32477599999947

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_002115.2_HLA-DRB1)

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

    29 S      0.708         4.468
    34 P      0.865         5.250
    38 W      0.626         4.069
    40 P      0.994**       5.888
    42 R      1.000**       5.917
    55 F      0.622         4.050
    57 D      0.994**       5.885
    61 Y      0.748         4.667
    66 S      1.000**       5.915
    76 F      0.664         4.256
    86 D      0.990**       5.868
    96 I      0.931         5.576
    99 Q      0.999**       5.913
   100 A      1.000**       5.917
   114 V      0.924         5.541
   115 V      1.000**       5.917
   133 S      0.799         4.919
   149 S      0.719         4.524
   257 S      0.985*        5.841
   258 G      0.780         4.828

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_002115.2_HLA-DRB1)

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

     3 C      0.556         2.943 +- 1.998
    13 T      0.578         3.033 +- 1.992
    29 S      0.907         4.380 +- 1.260
    33 R      0.770         3.824 +- 1.740
    34 P      0.956*        4.582 +- 0.985
    38 W      0.924         4.438 +- 1.152
    40 P      0.998**       4.751 +- 0.609
    42 R      1.000**       4.758 +- 0.585
    55 F      0.921         4.426 +- 1.167
    57 D      0.999**       4.753 +- 0.599
    61 Y      0.920         4.435 +- 1.194
    66 S      1.000**       4.758 +- 0.587
    76 F      0.930         4.465 +- 1.120
    85 P      0.671         3.415 +- 1.913
    86 D      0.998**       4.751 +- 0.605
    89 Y      0.855         4.158 +- 1.452
    96 I      0.987*        4.705 +- 0.719
    99 Q      1.000**       4.758 +- 0.587
   100 A      1.000**       4.758 +- 0.585
   106 T      0.790         3.896 +- 1.651
   107 Y      0.821         4.020 +- 1.557
   113 G      0.808         3.961 +- 1.578
   114 V      0.979*        4.674 +- 0.802
   115 V      1.000**       4.758 +- 0.585
   119 T      0.725         3.635 +- 1.829
   133 S      0.935         4.497 +- 1.114
   149 S      0.924         4.448 +- 1.166
   178 Q      0.814         3.985 +- 1.563
   195 R      0.690         3.487 +- 1.823
   257 S      0.995**       4.738 +- 0.648
   258 G      0.928         4.471 +- 1.151
   262 T      0.760         3.780 +- 1.762
   263 G      0.696         3.520 +- 1.880