--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 20:44:43 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-DPA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/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 -4005.41 -4044.09
2 -4007.06 -4033.22
--------------------------------------
TOTAL -4005.93 -4043.39
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DPA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/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} 1.004965 0.004610 0.879000 1.141000 1.002000 1.001
r(A<->C){all} 0.071255 0.000162 0.048282 0.097858 0.070566 1.000
r(A<->G){all} 0.341388 0.000860 0.284026 0.399771 0.340843 1.001
r(A<->T){all} 0.104146 0.000317 0.071971 0.140879 0.103169 1.001
r(C<->G){all} 0.075597 0.000122 0.055638 0.099142 0.075060 1.000
r(C<->T){all} 0.349116 0.000880 0.292641 0.408073 0.348655 1.002
r(G<->T){all} 0.058497 0.000131 0.037769 0.083020 0.057815 1.000
pi(A){all} 0.212647 0.000161 0.188690 0.238160 0.212224 1.001
pi(C){all} 0.289760 0.000194 0.262968 0.317792 0.289606 1.000
pi(G){all} 0.263707 0.000188 0.237280 0.290920 0.263680 1.000
pi(T){all} 0.233887 0.000169 0.208459 0.259934 0.233922 1.000
alpha{1,2} 0.562699 0.026756 0.334182 0.961066 0.534052 1.000
alpha{3} 15.277322 1282.281681 1.043976 150.291946 2.774631 1.000
pinvar{all} 0.242573 0.006890 0.057877 0.383040 0.250532 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 -3785.131161
Model 7: beta -3804.02363
Model 1: NearlyNeutral -3802.171207
Model 2: PositiveSelection -3785.725264
Model 2 vs 1 32.89188599999943
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_291032.2_HLA-DPA1)
Pr(w>1) post mean +- SE for w
36 A 1.000** 11.101
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_291032.2_HLA-DPA1)
Pr(w>1) post mean +- SE for w
36 A 1.000** 4.984 +- 1.674
47 F 0.635 3.223 +- 1.929
56 M 0.895 4.455 +- 1.887
90 I 0.735 3.636 +- 1.909
Model 8 vs 7 37.78493800000069
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_291032.2_HLA-DPA1)
Pr(w>1) post mean +- SE for w
21 R 0.522 2.346
36 A 1.000** 3.775
47 F 0.867 3.388
56 M 0.978* 3.712
90 I 0.927 3.563
93 N 0.828 3.278
98 L 0.688 2.872
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_291032.2_HLA-DPA1)
Pr(w>1) post mean +- SE for w
21 R 0.670 2.643 +- 1.430
36 A 1.000** 3.563 +- 0.706
47 F 0.922 3.346 +- 0.980
56 M 0.988* 3.530 +- 0.757
90 I 0.958* 3.446 +- 0.870
93 N 0.900 3.257 +- 1.007
98 L 0.818 3.013 +- 1.163
