--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 20:44:43 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-DPA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/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       -4005.41          -4044.09
2       -4007.06          -4033.22
--------------------------------------
TOTAL     -4005.93          -4043.39
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DPA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/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}           1.004965      0.004610      0.879000      1.141000      1.002000      1.001
r(A<->C){all}     0.071255      0.000162      0.048282      0.097858      0.070566      1.000
r(A<->G){all}     0.341388      0.000860      0.284026      0.399771      0.340843      1.001
r(A<->T){all}     0.104146      0.000317      0.071971      0.140879      0.103169      1.001
r(C<->G){all}     0.075597      0.000122      0.055638      0.099142      0.075060      1.000
r(C<->T){all}     0.349116      0.000880      0.292641      0.408073      0.348655      1.002
r(G<->T){all}     0.058497      0.000131      0.037769      0.083020      0.057815      1.000
pi(A){all}        0.212647      0.000161      0.188690      0.238160      0.212224      1.001
pi(C){all}        0.289760      0.000194      0.262968      0.317792      0.289606      1.000
pi(G){all}        0.263707      0.000188      0.237280      0.290920      0.263680      1.000
pi(T){all}        0.233887      0.000169      0.208459      0.259934      0.233922      1.000
alpha{1,2}        0.562699      0.026756      0.334182      0.961066      0.534052      1.000
alpha{3}         15.277322   1282.281681      1.043976    150.291946      2.774631      1.000
pinvar{all}       0.242573      0.006890      0.057877      0.383040      0.250532      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	-3785.131161
Model 7: beta	-3804.02363
Model 1: NearlyNeutral	-3802.171207
Model 2: PositiveSelection	-3785.725264


Model 2 vs 1	32.89188599999943

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_291032.2_HLA-DPA1)

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

    36 A      1.000**       11.101

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_291032.2_HLA-DPA1)

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

    36 A      1.000**       4.984 +- 1.674
    47 F      0.635         3.223 +- 1.929
    56 M      0.895         4.455 +- 1.887
    90 I      0.735         3.636 +- 1.909


Model 8 vs 7	37.78493800000069

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_291032.2_HLA-DPA1)

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

    21 R      0.522         2.346
    36 A      1.000**       3.775
    47 F      0.867         3.388
    56 M      0.978*        3.712
    90 I      0.927         3.563
    93 N      0.828         3.278
    98 L      0.688         2.872

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_291032.2_HLA-DPA1)

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

    21 R      0.670         2.643 +- 1.430
    36 A      1.000**       3.563 +- 0.706
    47 F      0.922         3.346 +- 0.980
    56 M      0.988*        3.530 +- 0.757
    90 I      0.958*        3.446 +- 0.870
    93 N      0.900         3.257 +- 1.007
    98 L      0.818         3.013 +- 1.163