--- 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
