--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Apr 12 01:12:45 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-E/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-E/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       -3585.38          -3603.86
2       -3585.34          -3604.67
--------------------------------------
TOTAL     -3585.36          -3604.35
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-E/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-E/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}           0.454646      0.001094      0.394000      0.523000      0.453000      1.002
r(A<->C){all}     0.091623      0.000340      0.058053      0.130208      0.090736      1.001
r(A<->G){all}     0.280642      0.000929      0.223083      0.342813      0.279684      1.000
r(A<->T){all}     0.146965      0.000896      0.092771      0.209560      0.145327      1.001
r(C<->G){all}     0.089806      0.000197      0.064316      0.119526      0.089177      1.001
r(C<->T){all}     0.284039      0.000995      0.225588      0.348399      0.283189      1.000
r(G<->T){all}     0.106925      0.000373      0.072371      0.146891      0.105936      1.000
pi(A){all}        0.205018      0.000121      0.183878      0.227103      0.204839      1.000
pi(C){all}        0.294485      0.000152      0.270514      0.318932      0.294500      1.001
pi(G){all}        0.320964      0.000169      0.295663      0.346301      0.320992      1.000
pi(T){all}        0.179533      0.000108      0.160089      0.200524      0.179376      1.001
alpha{1,2}        0.878805     18.509750      0.314995      1.745207      0.625052      1.000
alpha{3}         96.624216   3406.951439      4.913938    194.573897     95.143201      1.000
pinvar{all}       0.419255      0.005973      0.250433      0.552914      0.425489      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	-2996.868094
Model 7: beta	-3011.491184
Model 1: NearlyNeutral	-3008.561247
Model 2: PositiveSelection	-2996.000173


Model 2 vs 1	25.12214800000038

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_005507.3_HLA-E)

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

     2 V      0.976*        6.438
     3 D      0.937         6.218
     4 G      0.977*        6.441
    96 R      0.790         5.399
   162 Q      0.646         4.596
   168 S      0.998**       6.560
   187 K      0.663         4.691
   200 E      0.697         4.879
   305 I      0.526         3.932
   306 A      0.642         4.573
   309 V      0.720         5.008

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_005507.3_HLA-E)

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

     2 V      0.976*        6.720 +- 1.869
     3 D      0.937         6.513 +- 2.145
     4 G      0.975*        6.722 +- 1.875
    96 R      0.768         5.351 +- 2.768
   162 Q      0.653         4.807 +- 3.075
   168 S      0.998**       6.837 +- 1.682
   187 K      0.659         4.793 +- 3.027
   200 E      0.675         4.799 +- 2.936
   305 I      0.520         3.914 +- 3.023
   306 A      0.640         4.678 +- 3.048
   309 V      0.720         5.181 +- 2.954


Model 8 vs 7	29.246180000000095

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_005507.3_HLA-E)

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

     2 V      0.985*        5.929
     3 D      0.955*        5.779
     4 G      0.982*        5.916
    96 R      0.888         5.435
   162 Q      0.721         4.576
   168 S      0.999**       6.000
   187 K      0.750         4.725
   200 E      0.809         5.032
   305 I      0.639         4.155
   306 A      0.731         4.630
   309 V      0.793         4.946

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_005507.3_HLA-E)

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

     2 V      0.988*        5.355 +- 1.456
     3 D      0.965*        5.262 +- 1.590
     4 G      0.983*        5.339 +- 1.486
    96 R      0.934         5.075 +- 1.721
   162 Q      0.803         4.515 +- 2.196
   168 S      0.999**       5.399 +- 1.388
   187 K      0.829         4.615 +- 2.115
   198 H      0.526         3.045 +- 2.240
   200 E      0.878         4.815 +- 1.937
   305 I      0.751         4.223 +- 2.264
   306 A      0.816         4.554 +- 2.148
   309 V      0.857         4.758 +- 2.038