--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 17:29:18 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-DMA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DMA/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       -3174.09          -3203.16
2       -3174.08          -3205.75
--------------------------------------
TOTAL     -3174.09          -3205.13
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DMA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DMA/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}           0.879200      0.004738      0.754000      1.022000      0.876000      1.001
r(A<->C){all}     0.051097      0.000172      0.028250      0.079462      0.050179      1.000
r(A<->G){all}     0.492558      0.001355      0.420635      0.563207      0.493026      1.003
r(A<->T){all}     0.065489      0.000244      0.038128      0.099284      0.064435      1.000
r(C<->G){all}     0.079659      0.000205      0.054389      0.110615      0.078879      1.000
r(C<->T){all}     0.273316      0.000977      0.215706      0.337289      0.271859      1.004
r(G<->T){all}     0.037881      0.000131      0.018150      0.062755      0.037027      1.000
pi(A){all}        0.210532      0.000163      0.186113      0.236323      0.210354      1.000
pi(C){all}        0.280727      0.000202      0.253261      0.308400      0.280482      1.000
pi(G){all}        0.246893      0.000187      0.220531      0.274179      0.246765      1.000
pi(T){all}        0.261849      0.000201      0.234799      0.290501      0.261568      1.003
alpha{1,2}        0.346654      0.005281      0.236515      0.514969      0.336064      1.000
alpha{3}         78.786982   3787.259058      2.929508    193.167370     67.485194      1.002
pinvar{all}       0.306216      0.003190      0.183208      0.406351      0.309745      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	-3108.292395
Model 7: beta	-3118.332344
Model 1: NearlyNeutral	-3117.284064
Model 2: PositiveSelection	-3108.415027


Model 2 vs 1	17.73807399999987

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_006111.2_HLA-DMA)

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

    56 S      0.664         3.096
   102 K      0.569         2.795
   103 E      0.841         3.654
   107 W      0.999**       4.154
   111 Q      0.584         2.842
   115 K      0.968*        4.057

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_006111.2_HLA-DMA)

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

    34 M      0.506         2.547 +- 1.692
    56 S      0.663         3.092 +- 1.718
   102 K      0.580         2.832 +- 1.757
   103 E      0.838         3.720 +- 1.567
   107 W      0.998**       4.274 +- 1.154
   111 Q      0.595         2.890 +- 1.764
   115 K      0.966*        4.182 +- 1.276


Model 8 vs 7	20.079897999999957

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_006111.2_HLA-DMA)

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

    27 V      0.612         2.723
    34 M      0.623         2.755
    56 S      0.769         3.184
    75 Q      0.543         2.517
   102 K      0.676         2.908
   103 E      0.899         3.564
   107 W      0.999**       3.855
   111 Q      0.688         2.943
   115 K      0.979*        3.796
   166 V      0.596         2.678

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_006111.2_HLA-DMA)

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

     7 Q      0.671         2.518 +- 1.389
    25 W      0.597         2.299 +- 1.387
    27 V      0.785         2.819 +- 1.275
    34 M      0.791         2.839 +- 1.272
    56 S      0.879         3.086 +- 1.154
    75 Q      0.727         2.662 +- 1.333
   102 K      0.815         2.916 +- 1.258
   103 E      0.949         3.279 +- 1.008
   107 W      0.999**       3.406 +- 0.865
   111 Q      0.822         2.937 +- 1.249
   115 K      0.986*        3.377 +- 0.906
   166 V      0.775         2.789 +- 1.282