--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 19:13:01 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-DOA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOA/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       -2757.44          -2788.61
2       -2757.47          -2787.53
--------------------------------------
TOTAL     -2757.46          -2788.21
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DOA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOA/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}           0.602435      0.003419      0.506000      0.731000      0.596000      1.002
r(A<->C){all}     0.077075      0.000284      0.047765      0.113191      0.075897      1.000
r(A<->G){all}     0.398909      0.001585      0.322753      0.478178      0.397974      1.000
r(A<->T){all}     0.052724      0.000327      0.022508      0.092134      0.051082      1.001
r(C<->G){all}     0.056924      0.000131      0.036467      0.081281      0.056235      1.001
r(C<->T){all}     0.375131      0.001453      0.301542      0.450926      0.375077      1.000
r(G<->T){all}     0.039237      0.000139      0.019236      0.064860      0.038177      1.000
pi(A){all}        0.192156      0.000165      0.167814      0.217376      0.191923      1.000
pi(C){all}        0.318384      0.000236      0.288596      0.349123      0.318251      1.000
pi(G){all}        0.278358      0.000222      0.249301      0.308066      0.278171      1.000
pi(T){all}        0.211102      0.000180      0.185775      0.238094      0.210662      1.000
alpha{1,2}       41.555327   3477.108527      0.472556    186.526295      4.233821      1.000
alpha{3}         64.383429   3898.802620      0.998690    191.245575     43.370592      1.001
pinvar{all}       0.505866      0.007391      0.274045      0.607628      0.529107      1.001
---------------------------------------------------------------------------------------------
* 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	-2686.922273
Model 7: beta	-2687.012962
Model 1: NearlyNeutral	-2687.955325
Model 2: PositiveSelection	-2687.955325


Model 2 vs 1	0.0

Model 8 vs 7	0.18137799999931303