--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 22:33:58 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-DQA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/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 -4577.54 -4610.97
2 -4578.11 -4609.41
--------------------------------------
TOTAL -4577.78 -4610.47
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DQA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/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} 1.396605 0.008219 1.233000 1.587000 1.393000 1.001
r(A<->C){all} 0.075266 0.000162 0.052370 0.102518 0.074623 1.000
r(A<->G){all} 0.313963 0.000766 0.261407 0.370456 0.313569 1.000
r(A<->T){all} 0.086774 0.000185 0.062252 0.115067 0.085893 1.000
r(C<->G){all} 0.115818 0.000198 0.089967 0.145236 0.115327 1.001
r(C<->T){all} 0.350246 0.000795 0.296403 0.406707 0.349545 1.000
r(G<->T){all} 0.057933 0.000105 0.039742 0.080026 0.057319 1.000
pi(A){all} 0.222839 0.000170 0.198424 0.248634 0.222540 1.000
pi(C){all} 0.252829 0.000172 0.227537 0.278672 0.252822 1.001
pi(G){all} 0.260793 0.000186 0.234362 0.288173 0.260787 1.000
pi(T){all} 0.263539 0.000182 0.237117 0.290085 0.263282 1.000
alpha{1,2} 0.404651 0.004949 0.297236 0.569814 0.394923 1.000
alpha{3} 2.045586 1.886431 1.045132 4.325206 1.816090 1.000
pinvar{all} 0.114547 0.003484 0.011136 0.232698 0.113230 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 -4422.145612
Model 7: beta -4452.694719
Model 1: NearlyNeutral -4450.300583
Model 2: PositiveSelection -4420.507966
Model 2 vs 1 59.58523400000013
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_002113.2_HLA-DQA1)
Pr(w>1) post mean +- SE for w
78 G 1.000** 9.709
90 V 0.752 7.551
91 A 1.000** 9.709
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_002113.2_HLA-DQA1)
Pr(w>1) post mean +- SE for w
78 G 1.000** 7.520 +- 1.833
90 V 0.951* 7.128 +- 2.249
91 A 1.000** 7.520 +- 1.833
Model 8 vs 7 61.09821399999964
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_002113.2_HLA-DQA1)
Pr(w>1) post mean +- SE for w
78 G 1.000** 8.767
90 V 0.860 7.675
91 A 1.000** 8.767
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_002113.2_HLA-DQA1)
Pr(w>1) post mean +- SE for w
41 F 0.799 3.597 +- 1.563
76 K 0.863 3.865 +- 1.470
78 G 1.000** 4.483 +- 1.149
90 V 0.996** 4.464 +- 1.164
91 A 1.000** 4.483 +- 1.149
98 M 0.877 3.913 +- 1.425
