--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Apr 12 00:15:24 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-DRA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRA/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 -3158.33 -3190.26
2 -3158.31 -3195.37
--------------------------------------
TOTAL -3158.32 -3194.68
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DRA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRA/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} 0.921735 0.005883 0.777000 1.077000 0.921000 1.000
r(A<->C){all} 0.083183 0.000256 0.054917 0.118241 0.082222 1.000
r(A<->G){all} 0.355278 0.001267 0.287351 0.426724 0.354586 1.000
r(A<->T){all} 0.077577 0.000275 0.048163 0.113386 0.076637 1.000
r(C<->G){all} 0.051837 0.000151 0.030392 0.078291 0.050846 1.000
r(C<->T){all} 0.379327 0.001301 0.310045 0.451075 0.378925 1.000
r(G<->T){all} 0.052799 0.000176 0.029649 0.081437 0.051842 1.000
pi(A){all} 0.241828 0.000193 0.215725 0.269873 0.241638 1.001
pi(C){all} 0.251255 0.000203 0.224156 0.280073 0.250988 1.000
pi(G){all} 0.270071 0.000213 0.242116 0.299504 0.269782 1.000
pi(T){all} 0.236846 0.000196 0.209434 0.264431 0.236763 1.001
alpha{1,2} 0.358049 0.007940 0.229864 0.560696 0.344065 1.000
alpha{3} 52.981062 3631.822526 1.507308 189.077301 21.103231 1.001
pinvar{all} 0.354695 0.004253 0.199105 0.460260 0.362883 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 -3087.681424
Model 7: beta -3092.96422
Model 1: NearlyNeutral -3091.227626
Model 2: PositiveSelection -3088.673021
Model 2 vs 1 5.109209999999621
Model 8 vs 7 10.565591999999924
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_061984.2_HLA-DRA)
Pr(w>1) post mean +- SE for w
3 I 0.911 2.086
8 V 0.697 1.748
24 W 0.717 1.773
40 N 0.714 1.777
44 S 0.741 1.811
62 A 0.966* 2.172
75 R 0.819 1.937
104 Y 0.609 1.608
143 N 0.836 1.970
148 R 0.993** 2.213
185 V 0.638 1.654
193 W 0.713 1.765
233 I 0.900 2.070
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_061984.2_HLA-DRA)
Pr(w>1) post mean +- SE for w
3 I 0.864 2.188 +- 0.782
8 V 0.624 1.729 +- 0.894
24 W 0.675 1.835 +- 0.923
40 N 0.637 1.753 +- 0.889
44 S 0.702 1.889 +- 0.917
62 A 0.939 2.323 +- 0.697
75 R 0.785 2.049 +- 0.873
104 Y 0.534 1.555 +- 0.879
143 N 0.763 1.994 +- 0.846
148 R 0.983* 2.393 +- 0.635
185 V 0.561 1.607 +- 0.885
193 W 0.671 1.828 +- 0.925
233 I 0.848 2.154 +- 0.793
