--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 23:25:20 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-DQB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/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 -4736.68 -4761.96
2 -4736.88 -4761.25
--------------------------------------
TOTAL -4736.78 -4761.67
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DQB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/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} 1.494988 0.010048 1.309000 1.700000 1.491000 1.000
r(A<->C){all} 0.097590 0.000215 0.070585 0.128878 0.096899 1.000
r(A<->G){all} 0.243611 0.000553 0.198660 0.291292 0.243298 1.000
r(A<->T){all} 0.111080 0.000331 0.078093 0.149320 0.110091 1.000
r(C<->G){all} 0.084797 0.000125 0.064467 0.108281 0.084417 1.001
r(C<->T){all} 0.371739 0.000831 0.317460 0.429537 0.371334 1.000
r(G<->T){all} 0.091182 0.000178 0.067025 0.118903 0.090761 1.000
pi(A){all} 0.213236 0.000168 0.188748 0.239925 0.212889 1.000
pi(C){all} 0.274979 0.000181 0.248934 0.301305 0.274816 1.001
pi(G){all} 0.310196 0.000195 0.282973 0.338299 0.310011 1.001
pi(T){all} 0.201590 0.000154 0.177545 0.227012 0.201313 1.000
alpha{1,2} 0.403163 0.004423 0.297946 0.554992 0.395285 1.000
alpha{3} 2.578861 30.190802 1.108606 5.598211 2.025743 1.000
pinvar{all} 0.138659 0.003439 0.022964 0.251119 0.140871 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 -4412.629266
Model 7: beta -4444.988725
Model 1: NearlyNeutral -4437.31931
Model 2: PositiveSelection -4417.335403
Model 2 vs 1 39.967813999999635
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_002114.3_HLA-DQB1)
Pr(w>1) post mean +- SE for w
15 V 0.592 2.237
40 F 0.912 2.908
44 G 0.937 2.961
57 L 1.000** 3.092
68 Y 0.818 2.711
88 D 0.997** 3.086
98 V 0.614 2.285
101 G 0.904 2.891
102 T 0.933 2.952
107 R 0.981* 3.051
112 V 0.838 2.753
114 F 0.858 2.795
116 G 0.835 2.746
121 R 0.510 2.037
194 R 0.648 2.354
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_002114.3_HLA-DQB1)
Pr(w>1) post mean +- SE for w
15 V 0.607 2.286 +- 1.113
40 F 0.909 2.953 +- 0.784
44 G 0.937 3.021 +- 0.720
57 L 1.000** 3.157 +- 0.513
68 Y 0.809 2.716 +- 0.951
88 D 0.997** 3.152 +- 0.524
98 V 0.611 2.265 +- 1.084
101 G 0.899 2.925 +- 0.806
102 T 0.930 3.001 +- 0.736
107 R 0.980* 3.118 +- 0.589
112 V 0.840 2.802 +- 0.914
114 F 0.856 2.835 +- 0.886
116 G 0.828 2.763 +- 0.926
121 R 0.525 2.078 +- 1.192
194 R 0.665 2.421 +- 1.095
Model 8 vs 7 64.71891800000049
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_002114.3_HLA-DQB1)
Pr(w>1) post mean +- SE for w
8 R 0.754 2.055
15 V 0.871 2.268
40 F 0.995** 2.503
44 G 0.995** 2.503
57 L 1.000** 2.512
68 Y 0.987* 2.489
69 A 0.869 2.271
86 R 0.725 1.998
88 D 1.000** 2.512
98 V 0.959* 2.437
101 G 0.995** 2.503
102 T 0.996** 2.504
107 R 0.998** 2.509
112 V 0.980* 2.476
113 A 0.616 1.795
114 F 0.986* 2.487
115 R 0.799 2.140
116 G 0.988* 2.491
117 I 0.654 1.870
121 R 0.714 1.948
169 V 0.705 1.951
194 R 0.891 2.306
247 R 0.657 1.858
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_002114.3_HLA-DQB1)
Pr(w>1) post mean +- SE for w
15 V 0.723 2.130 +- 0.917
40 F 0.970* 2.626 +- 0.491
44 G 0.976* 2.639 +- 0.476
57 L 1.000** 2.684 +- 0.390
68 Y 0.932 2.549 +- 0.586
69 A 0.637 1.953 +- 0.903
88 D 0.999** 2.682 +- 0.393
98 V 0.830 2.338 +- 0.757
101 G 0.968* 2.622 +- 0.495
102 T 0.976* 2.638 +- 0.474
107 R 0.991** 2.668 +- 0.424
112 V 0.927 2.544 +- 0.608
114 F 0.940 2.568 +- 0.574
115 R 0.535 1.747 +- 0.916
116 G 0.939 2.563 +- 0.572
121 R 0.564 1.786 +- 1.052
194 R 0.762 2.214 +- 0.886
