--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Apr 12 00:15:24 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-DRA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRA/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       -3158.33          -3190.26
2       -3158.31          -3195.37
--------------------------------------
TOTAL     -3158.32          -3194.68
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DRA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRA/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}           0.921735      0.005883      0.777000      1.077000      0.921000      1.000
r(A<->C){all}     0.083183      0.000256      0.054917      0.118241      0.082222      1.000
r(A<->G){all}     0.355278      0.001267      0.287351      0.426724      0.354586      1.000
r(A<->T){all}     0.077577      0.000275      0.048163      0.113386      0.076637      1.000
r(C<->G){all}     0.051837      0.000151      0.030392      0.078291      0.050846      1.000
r(C<->T){all}     0.379327      0.001301      0.310045      0.451075      0.378925      1.000
r(G<->T){all}     0.052799      0.000176      0.029649      0.081437      0.051842      1.000
pi(A){all}        0.241828      0.000193      0.215725      0.269873      0.241638      1.001
pi(C){all}        0.251255      0.000203      0.224156      0.280073      0.250988      1.000
pi(G){all}        0.270071      0.000213      0.242116      0.299504      0.269782      1.000
pi(T){all}        0.236846      0.000196      0.209434      0.264431      0.236763      1.001
alpha{1,2}        0.358049      0.007940      0.229864      0.560696      0.344065      1.000
alpha{3}         52.981062   3631.822526      1.507308    189.077301     21.103231      1.001
pinvar{all}       0.354695      0.004253      0.199105      0.460260      0.362883      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	-3087.681424
Model 7: beta	-3092.96422
Model 1: NearlyNeutral	-3091.227626
Model 2: PositiveSelection	-3088.673021


Model 2 vs 1	5.109209999999621

Model 8 vs 7	10.565591999999924

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_061984.2_HLA-DRA)

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

     3 I      0.911         2.086
     8 V      0.697         1.748
    24 W      0.717         1.773
    40 N      0.714         1.777
    44 S      0.741         1.811
    62 A      0.966*        2.172
    75 R      0.819         1.937
   104 Y      0.609         1.608
   143 N      0.836         1.970
   148 R      0.993**       2.213
   185 V      0.638         1.654
   193 W      0.713         1.765
   233 I      0.900         2.070

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_061984.2_HLA-DRA)

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

     3 I      0.864         2.188 +- 0.782
     8 V      0.624         1.729 +- 0.894
    24 W      0.675         1.835 +- 0.923
    40 N      0.637         1.753 +- 0.889
    44 S      0.702         1.889 +- 0.917
    62 A      0.939         2.323 +- 0.697
    75 R      0.785         2.049 +- 0.873
   104 Y      0.534         1.555 +- 0.879
   143 N      0.763         1.994 +- 0.846
   148 R      0.983*        2.393 +- 0.635
   185 V      0.561         1.607 +- 0.885
   193 W      0.671         1.828 +- 0.925
   233 I      0.848         2.154 +- 0.793