--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 22:33:58 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-DQA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/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       -4577.54          -4610.97
2       -4578.11          -4609.41
--------------------------------------
TOTAL     -4577.78          -4610.47
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DQA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/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}           1.396605      0.008219      1.233000      1.587000      1.393000      1.001
r(A<->C){all}     0.075266      0.000162      0.052370      0.102518      0.074623      1.000
r(A<->G){all}     0.313963      0.000766      0.261407      0.370456      0.313569      1.000
r(A<->T){all}     0.086774      0.000185      0.062252      0.115067      0.085893      1.000
r(C<->G){all}     0.115818      0.000198      0.089967      0.145236      0.115327      1.001
r(C<->T){all}     0.350246      0.000795      0.296403      0.406707      0.349545      1.000
r(G<->T){all}     0.057933      0.000105      0.039742      0.080026      0.057319      1.000
pi(A){all}        0.222839      0.000170      0.198424      0.248634      0.222540      1.000
pi(C){all}        0.252829      0.000172      0.227537      0.278672      0.252822      1.001
pi(G){all}        0.260793      0.000186      0.234362      0.288173      0.260787      1.000
pi(T){all}        0.263539      0.000182      0.237117      0.290085      0.263282      1.000
alpha{1,2}        0.404651      0.004949      0.297236      0.569814      0.394923      1.000
alpha{3}          2.045586      1.886431      1.045132      4.325206      1.816090      1.000
pinvar{all}       0.114547      0.003484      0.011136      0.232698      0.113230      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	-4422.145612
Model 7: beta	-4452.694719
Model 1: NearlyNeutral	-4450.300583
Model 2: PositiveSelection	-4420.507966


Model 2 vs 1	59.58523400000013

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_002113.2_HLA-DQA1)

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

    78 G      1.000**       9.709
    90 V      0.752         7.551
    91 A      1.000**       9.709

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_002113.2_HLA-DQA1)

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

    78 G      1.000**       7.520 +- 1.833
    90 V      0.951*        7.128 +- 2.249
    91 A      1.000**       7.520 +- 1.833


Model 8 vs 7	61.09821399999964

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_002113.2_HLA-DQA1)

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

    78 G      1.000**       8.767
    90 V      0.860         7.675
    91 A      1.000**       8.767

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_002113.2_HLA-DQA1)

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

    41 F      0.799         3.597 +- 1.563
    76 K      0.863         3.865 +- 1.470
    78 G      1.000**       4.483 +- 1.149
    90 V      0.996**       4.464 +- 1.164
    91 A      1.000**       4.483 +- 1.149
    98 M      0.877         3.913 +- 1.425