--- 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
