--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 23:34:23 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-DQB2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB2/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       -2037.30          -2052.44
2       -2037.47          -2054.94
--------------------------------------
TOTAL     -2037.38          -2054.32
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DQB2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB2/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}           0.332268      0.001951      0.261000      0.434000      0.327000      1.000
r(A<->C){all}     0.081725      0.000615      0.038843      0.135235      0.079424      1.000
r(A<->G){all}     0.261268      0.001789      0.183520      0.348225      0.259638      1.000
r(A<->T){all}     0.062053      0.000837      0.014580      0.126068      0.059100      1.001
r(C<->G){all}     0.088577      0.000548      0.047506      0.138371      0.086899      1.000
r(C<->T){all}     0.406853      0.002884      0.307226      0.515548      0.404763      1.000
r(G<->T){all}     0.099524      0.000811      0.049363      0.162299      0.097413      1.000
pi(A){all}        0.209974      0.000175      0.184454      0.236328      0.209752      1.000
pi(C){all}        0.276586      0.000207      0.248659      0.304914      0.276544      1.000
pi(G){all}        0.313088      0.000231      0.283459      0.343260      0.312841      1.000
pi(T){all}        0.200353      0.000166      0.175767      0.226280      0.200249      1.000
alpha{1,2}       93.297168   3646.579991      1.844282    194.456566     92.055876      1.001
alpha{3}        101.311825   3222.281802      8.074997    195.348397    100.635390      1.000
pinvar{all}       0.631657      0.003205      0.499569      0.721356      0.638699      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	-1946.637262
Model 7: beta	-1947.424052
Model 1: NearlyNeutral	-1946.963447
Model 2: PositiveSelection	-1946.627808


Model 2 vs 1	0.6712780000002567

Model 8 vs 7	1.57358000000022