--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 20:01:36 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-DOB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOB/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       -3314.80          -3342.00
2       -3314.49          -3342.64
--------------------------------------
TOTAL     -3314.63          -3342.37
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DOB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOB/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}           0.664970      0.002172      0.581000      0.764000      0.662000      1.005
r(A<->C){all}     0.097177      0.000324      0.064769      0.135653      0.096288      1.000
r(A<->G){all}     0.270211      0.000726      0.219817      0.326032      0.269522      1.000
r(A<->T){all}     0.048156      0.000175      0.025365      0.076837      0.047087      1.001
r(C<->G){all}     0.141512      0.000345      0.107435      0.179443      0.140725      1.000
r(C<->T){all}     0.390233      0.001013      0.329916      0.453873      0.389666      1.000
r(G<->T){all}     0.052711      0.000147      0.030822      0.078338      0.052063      1.000
pi(A){all}        0.219441      0.000158      0.195434      0.244074      0.219162      1.000
pi(C){all}        0.244527      0.000160      0.220144      0.269462      0.244371      1.000
pi(G){all}        0.288959      0.000189      0.262353      0.316546      0.289040      1.000
pi(T){all}        0.247073      0.000172      0.221702      0.273338      0.246906      1.000
alpha{1,2}       43.368315   3540.845816      0.779146    187.655306      5.397278      1.015
alpha{3}         93.193195   3581.724551      3.278866    194.536091     91.022956      1.005
pinvar{all}       0.367901      0.005195      0.197152      0.473994      0.380638      1.010
---------------------------------------------------------------------------------------------
* 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	-2704.917655
Model 7: beta	-2708.679026
Model 1: NearlyNeutral	-2707.138142
Model 2: PositiveSelection	-2704.790433


Model 2 vs 1	4.695417999999336

Model 8 vs 7	7.522741999999198

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_002111.1_HLA-DOB)

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

     7 S      0.637         2.360
    43 R      0.511         2.047
    56 K      0.988*        3.228
    67 S      0.827         2.835
   232 L      0.518         2.066

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_002111.1_HLA-DOB)

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

     7 S      0.767         2.239 +- 1.106
    43 R      0.691         2.065 +- 1.120
    56 K      0.981*        2.642 +- 0.879
    67 S      0.881         2.471 +- 1.010
   227 S      0.620         1.931 +- 1.172
   232 L      0.695         2.076 +- 1.120