--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 23:25:20 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-DQB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/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       -4736.68          -4761.96
2       -4736.88          -4761.25
--------------------------------------
TOTAL     -4736.78          -4761.67
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DQB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/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}           1.494988      0.010048      1.309000      1.700000      1.491000      1.000
r(A<->C){all}     0.097590      0.000215      0.070585      0.128878      0.096899      1.000
r(A<->G){all}     0.243611      0.000553      0.198660      0.291292      0.243298      1.000
r(A<->T){all}     0.111080      0.000331      0.078093      0.149320      0.110091      1.000
r(C<->G){all}     0.084797      0.000125      0.064467      0.108281      0.084417      1.001
r(C<->T){all}     0.371739      0.000831      0.317460      0.429537      0.371334      1.000
r(G<->T){all}     0.091182      0.000178      0.067025      0.118903      0.090761      1.000
pi(A){all}        0.213236      0.000168      0.188748      0.239925      0.212889      1.000
pi(C){all}        0.274979      0.000181      0.248934      0.301305      0.274816      1.001
pi(G){all}        0.310196      0.000195      0.282973      0.338299      0.310011      1.001
pi(T){all}        0.201590      0.000154      0.177545      0.227012      0.201313      1.000
alpha{1,2}        0.403163      0.004423      0.297946      0.554992      0.395285      1.000
alpha{3}          2.578861     30.190802      1.108606      5.598211      2.025743      1.000
pinvar{all}       0.138659      0.003439      0.022964      0.251119      0.140871      1.000
---------------------------------------------------------------------------------------------
* 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	-4412.629266
Model 7: beta	-4444.988725
Model 1: NearlyNeutral	-4437.31931
Model 2: PositiveSelection	-4417.335403


Model 2 vs 1	39.967813999999635

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_002114.3_HLA-DQB1)

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

    15 V      0.592         2.237
    40 F      0.912         2.908
    44 G      0.937         2.961
    57 L      1.000**       3.092
    68 Y      0.818         2.711
    88 D      0.997**       3.086
    98 V      0.614         2.285
   101 G      0.904         2.891
   102 T      0.933         2.952
   107 R      0.981*        3.051
   112 V      0.838         2.753
   114 F      0.858         2.795
   116 G      0.835         2.746
   121 R      0.510         2.037
   194 R      0.648         2.354

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_002114.3_HLA-DQB1)

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

    15 V      0.607         2.286 +- 1.113
    40 F      0.909         2.953 +- 0.784
    44 G      0.937         3.021 +- 0.720
    57 L      1.000**       3.157 +- 0.513
    68 Y      0.809         2.716 +- 0.951
    88 D      0.997**       3.152 +- 0.524
    98 V      0.611         2.265 +- 1.084
   101 G      0.899         2.925 +- 0.806
   102 T      0.930         3.001 +- 0.736
   107 R      0.980*        3.118 +- 0.589
   112 V      0.840         2.802 +- 0.914
   114 F      0.856         2.835 +- 0.886
   116 G      0.828         2.763 +- 0.926
   121 R      0.525         2.078 +- 1.192
   194 R      0.665         2.421 +- 1.095


Model 8 vs 7	64.71891800000049

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_002114.3_HLA-DQB1)

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

     8 R      0.754         2.055
    15 V      0.871         2.268
    40 F      0.995**       2.503
    44 G      0.995**       2.503
    57 L      1.000**       2.512
    68 Y      0.987*        2.489
    69 A      0.869         2.271
    86 R      0.725         1.998
    88 D      1.000**       2.512
    98 V      0.959*        2.437
   101 G      0.995**       2.503
   102 T      0.996**       2.504
   107 R      0.998**       2.509
   112 V      0.980*        2.476
   113 A      0.616         1.795
   114 F      0.986*        2.487
   115 R      0.799         2.140
   116 G      0.988*        2.491
   117 I      0.654         1.870
   121 R      0.714         1.948
   169 V      0.705         1.951
   194 R      0.891         2.306
   247 R      0.657         1.858

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_002114.3_HLA-DQB1)

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

    15 V      0.723         2.130 +- 0.917
    40 F      0.970*        2.626 +- 0.491
    44 G      0.976*        2.639 +- 0.476
    57 L      1.000**       2.684 +- 0.390
    68 Y      0.932         2.549 +- 0.586
    69 A      0.637         1.953 +- 0.903
    88 D      0.999**       2.682 +- 0.393
    98 V      0.830         2.338 +- 0.757
   101 G      0.968*        2.622 +- 0.495
   102 T      0.976*        2.638 +- 0.474
   107 R      0.991**       2.668 +- 0.424
   112 V      0.927         2.544 +- 0.608
   114 F      0.940         2.568 +- 0.574
   115 R      0.535         1.747 +- 0.916
   116 G      0.939         2.563 +- 0.572
   121 R      0.564         1.786 +- 1.052
   194 R      0.762         2.214 +- 0.886