--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 22:39:45 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-DQA2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA2/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 -1621.96 -1635.10
2 -1622.04 -1635.29
--------------------------------------
TOTAL -1622.00 -1635.20
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DQA2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA2/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} 0.150195 0.000323 0.118000 0.189000 0.149000 1.000
r(A<->C){all} 0.093492 0.000961 0.042005 0.162026 0.090481 1.000
r(A<->G){all} 0.358685 0.003059 0.255512 0.469584 0.357358 1.003
r(A<->T){all} 0.052658 0.000659 0.013369 0.113591 0.049067 1.000
r(C<->G){all} 0.014515 0.000154 0.000459 0.045676 0.011230 1.001
r(C<->T){all} 0.407011 0.003196 0.300013 0.521326 0.405729 1.001
r(G<->T){all} 0.073640 0.000684 0.030800 0.131475 0.070858 1.003
pi(A){all} 0.216009 0.000208 0.188822 0.244559 0.215721 1.001
pi(C){all} 0.267102 0.000235 0.237644 0.297986 0.266735 1.000
pi(G){all} 0.253296 0.000227 0.224413 0.283605 0.252868 1.000
pi(T){all} 0.263593 0.000227 0.234750 0.293549 0.263328 1.000
alpha{1,2} 96.129957 3509.943855 2.413238 194.553511 94.952352 1.000
alpha{3} 99.566418 3270.631513 6.520508 194.775279 98.404751 1.000
pinvar{all} 0.621317 0.012019 0.347806 0.773164 0.642304 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 -1564.570029
Model 7: beta -1564.570029
Model 1: NearlyNeutral -1564.60341
Model 2: PositiveSelection -1564.60341
Model 2 vs 1 0.0
Model 8 vs 7 0.0
