--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 21:27:29 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-DPB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/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       -4411.57          -4439.47
2       -4412.00          -4437.69
--------------------------------------
TOTAL     -4411.76          -4438.94
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DPB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/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}           1.311948      0.007611      1.153000      1.496000      1.307000      1.000
r(A<->C){all}     0.095493      0.000219      0.068544      0.126381      0.094675      1.000
r(A<->G){all}     0.251606      0.000629      0.204519      0.302783      0.250939      1.000
r(A<->T){all}     0.131658      0.000404      0.094393      0.173911      0.130884      1.002
r(C<->G){all}     0.088068      0.000142      0.066288      0.113269      0.087352      1.001
r(C<->T){all}     0.352732      0.000880      0.295231      0.410377      0.352657      1.000
r(G<->T){all}     0.080443      0.000174      0.056402      0.108313      0.079709      1.001
pi(A){all}        0.225367      0.000179      0.199610      0.252287      0.225029      1.000
pi(C){all}        0.274419      0.000199      0.247549      0.302189      0.274053      1.000
pi(G){all}        0.317525      0.000211      0.289375      0.346309      0.317246      1.000
pi(T){all}        0.182689      0.000147      0.159618      0.207011      0.182315      1.000
alpha{1,2}        0.401000      0.005573      0.282508      0.577192      0.391201      1.000
alpha{3}          4.420312    207.782930      1.028336     16.983666      2.132486      1.004
pinvar{all}       0.234107      0.003978      0.100442      0.346728      0.237641      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	-4296.78762
Model 7: beta	-4339.577445
Model 1: NearlyNeutral	-4331.797585
Model 2: PositiveSelection	-4297.35627


Model 2 vs 1	68.88263000000006

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_002112.3_HLA-DPB1)

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

    10 R      0.760         3.586
    24 S      0.531         2.809
    37 F      0.658         3.239
    39 G      1.000**       4.405
    41 Q      0.984*        4.349
    63 F      0.902         4.071
    83 A      1.000**       4.404
    90 I      1.000**       4.405
    93 E      0.952*        4.240
   254 A      0.976*        4.323

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_002112.3_HLA-DPB1)

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

    10 R      0.704         3.190 +- 1.556
    24 S      0.567         2.839 +- 1.768
    37 F      0.640         2.973 +- 1.600
    39 G      1.000**       4.552 +- 1.223
    41 Q      0.976*        4.431 +- 1.271
    63 F      0.848         3.796 +- 1.455
    83 A      1.000**       4.551 +- 1.224
    90 I      1.000**       4.552 +- 1.223
    93 E      0.915         4.107 +- 1.358
   254 A      0.975*        4.449 +- 1.310


Model 8 vs 7	85.57964999999967

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_002112.3_HLA-DPB1)

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

     7 A      0.658         2.290
     8 A      0.899         2.849
    10 R      0.990*        3.055
    15 T      0.745         2.498
    24 S      0.866         2.766
    36 L      0.935         2.931
    37 F      0.978*        3.029
    39 G      1.000**       3.078
    41 Q      0.999**       3.075
    46 F      0.705         2.387
    52 F      0.531         1.995
    63 F      0.995**       3.067
    64 A      0.890         2.829
    83 A      1.000**       3.078
    90 I      1.000**       3.078
    93 E      0.998**       3.073
    94 K      0.897         2.844
    97 V      0.805         2.634
   117 R      0.667         2.287
   254 A      0.996**       3.069

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_002112.3_HLA-DPB1)

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

     8 A      0.678         2.535 +- 1.239
    10 R      0.955*        3.371 +- 0.829
    24 S      0.771         2.847 +- 1.251
    36 L      0.793         2.882 +- 1.163
    37 F      0.921         3.267 +- 0.932
    39 G      1.000**       3.511 +- 0.664
    41 Q      0.996**       3.501 +- 0.681
    46 F      0.520         2.100 +- 1.322
    63 F      0.982*        3.456 +- 0.739
    64 A      0.712         2.652 +- 1.248
    83 A      1.000**       3.511 +- 0.665
    90 I      1.000**       3.511 +- 0.664
    93 E      0.991**       3.485 +- 0.701
    94 K      0.677         2.536 +- 1.242
    97 V      0.541         2.151 +- 1.257
   117 R      0.520         2.105 +- 1.364
   254 A      0.992**       3.489 +- 0.702