--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 20:01:36 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-DOB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOB/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 -3314.80 -3342.00
2 -3314.49 -3342.64
--------------------------------------
TOTAL -3314.63 -3342.37
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DOB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOB/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} 0.664970 0.002172 0.581000 0.764000 0.662000 1.005
r(A<->C){all} 0.097177 0.000324 0.064769 0.135653 0.096288 1.000
r(A<->G){all} 0.270211 0.000726 0.219817 0.326032 0.269522 1.000
r(A<->T){all} 0.048156 0.000175 0.025365 0.076837 0.047087 1.001
r(C<->G){all} 0.141512 0.000345 0.107435 0.179443 0.140725 1.000
r(C<->T){all} 0.390233 0.001013 0.329916 0.453873 0.389666 1.000
r(G<->T){all} 0.052711 0.000147 0.030822 0.078338 0.052063 1.000
pi(A){all} 0.219441 0.000158 0.195434 0.244074 0.219162 1.000
pi(C){all} 0.244527 0.000160 0.220144 0.269462 0.244371 1.000
pi(G){all} 0.288959 0.000189 0.262353 0.316546 0.289040 1.000
pi(T){all} 0.247073 0.000172 0.221702 0.273338 0.246906 1.000
alpha{1,2} 43.368315 3540.845816 0.779146 187.655306 5.397278 1.015
alpha{3} 93.193195 3581.724551 3.278866 194.536091 91.022956 1.005
pinvar{all} 0.367901 0.005195 0.197152 0.473994 0.380638 1.010
---------------------------------------------------------------------------------------------
* 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 -2704.917655
Model 7: beta -2708.679026
Model 1: NearlyNeutral -2707.138142
Model 2: PositiveSelection -2704.790433
Model 2 vs 1 4.695417999999336
Model 8 vs 7 7.522741999999198
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_002111.1_HLA-DOB)
Pr(w>1) post mean +- SE for w
7 S 0.637 2.360
43 R 0.511 2.047
56 K 0.988* 3.228
67 S 0.827 2.835
232 L 0.518 2.066
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_002111.1_HLA-DOB)
Pr(w>1) post mean +- SE for w
7 S 0.767 2.239 +- 1.106
43 R 0.691 2.065 +- 1.120
56 K 0.981* 2.642 +- 0.879
67 S 0.881 2.471 +- 1.010
227 S 0.620 1.931 +- 1.172
232 L 0.695 2.076 +- 1.120
