--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Apr 12 00:38:25 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-DRB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/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 -3046.22 -3074.68
2 -3046.67 -3070.64
--------------------------------------
TOTAL -3046.42 -3074.00
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DRB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/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} 0.643768 0.002956 0.544000 0.758000 0.642000 1.000
r(A<->C){all} 0.118655 0.000467 0.079572 0.164732 0.117636 1.000
r(A<->G){all} 0.197078 0.000680 0.149119 0.251845 0.195873 1.000
r(A<->T){all} 0.210508 0.000995 0.152378 0.275912 0.209360 1.000
r(C<->G){all} 0.118134 0.000340 0.084230 0.156392 0.117161 1.000
r(C<->T){all} 0.233516 0.000985 0.176175 0.297884 0.232207 1.000
r(G<->T){all} 0.122109 0.000427 0.084644 0.165890 0.121396 1.000
pi(A){all} 0.217459 0.000182 0.191887 0.244868 0.217195 1.000
pi(C){all} 0.255244 0.000202 0.228017 0.283252 0.254923 1.000
pi(G){all} 0.323233 0.000231 0.293790 0.353179 0.323159 1.000
pi(T){all} 0.204063 0.000168 0.179256 0.230097 0.203913 1.000
alpha{1,2} 0.791847 0.139134 0.363445 1.701675 0.707111 1.001
alpha{3} 3.496540 245.027947 0.505964 12.489141 1.189538 1.000
pinvar{all} 0.511124 0.005041 0.351044 0.628224 0.519164 1.001
---------------------------------------------------------------------------------------------
* 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 -2996.74708
Model 7: beta -3049.409468
Model 1: NearlyNeutral -3047.104289
Model 2: PositiveSelection -2996.103937
Model 2 vs 1 102.00070400000004
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_002115.2_HLA-DRB1)
Pr(w>1) post mean +- SE for w
29 S 0.662 4.319
34 P 0.842 5.223
38 W 0.526 3.638
40 P 0.993** 5.978
42 R 1.000** 6.014
55 F 0.525 3.633
57 D 0.990** 5.965
61 Y 0.707 4.543
66 S 0.999** 6.011
76 F 0.573 3.871
86 D 0.985* 5.937
96 I 0.901 5.518
99 Q 0.999** 6.009
100 A 1.000** 6.014
114 V 0.905 5.536
115 V 1.000** 6.014
133 S 0.765 4.838
149 S 0.659 4.304
257 S 0.981* 5.918
258 G 0.744 4.733
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_002115.2_HLA-DRB1)
Pr(w>1) post mean +- SE for w
29 S 0.604 4.177 +- 2.697
34 P 0.814 5.386 +- 2.317
40 P 0.992** 6.394 +- 1.207
42 R 1.000** 6.439 +- 1.108
57 D 0.984* 6.341 +- 1.286
61 Y 0.653 4.454 +- 2.659
66 S 0.999** 6.434 +- 1.118
86 D 0.975* 6.285 +- 1.375
96 I 0.845 5.493 +- 2.151
99 Q 0.999** 6.431 +- 1.124
100 A 1.000** 6.439 +- 1.108
114 V 0.880 5.749 +- 2.029
115 V 1.000** 6.439 +- 1.108
133 S 0.723 4.864 +- 2.559
149 S 0.596 4.119 +- 2.689
257 S 0.978* 6.320 +- 1.352
258 G 0.700 4.733 +- 2.602
Model 8 vs 7 105.32477599999947
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_002115.2_HLA-DRB1)
Pr(w>1) post mean +- SE for w
29 S 0.708 4.468
34 P 0.865 5.250
38 W 0.626 4.069
40 P 0.994** 5.888
42 R 1.000** 5.917
55 F 0.622 4.050
57 D 0.994** 5.885
61 Y 0.748 4.667
66 S 1.000** 5.915
76 F 0.664 4.256
86 D 0.990** 5.868
96 I 0.931 5.576
99 Q 0.999** 5.913
100 A 1.000** 5.917
114 V 0.924 5.541
115 V 1.000** 5.917
133 S 0.799 4.919
149 S 0.719 4.524
257 S 0.985* 5.841
258 G 0.780 4.828
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_002115.2_HLA-DRB1)
Pr(w>1) post mean +- SE for w
3 C 0.556 2.943 +- 1.998
13 T 0.578 3.033 +- 1.992
29 S 0.907 4.380 +- 1.260
33 R 0.770 3.824 +- 1.740
34 P 0.956* 4.582 +- 0.985
38 W 0.924 4.438 +- 1.152
40 P 0.998** 4.751 +- 0.609
42 R 1.000** 4.758 +- 0.585
55 F 0.921 4.426 +- 1.167
57 D 0.999** 4.753 +- 0.599
61 Y 0.920 4.435 +- 1.194
66 S 1.000** 4.758 +- 0.587
76 F 0.930 4.465 +- 1.120
85 P 0.671 3.415 +- 1.913
86 D 0.998** 4.751 +- 0.605
89 Y 0.855 4.158 +- 1.452
96 I 0.987* 4.705 +- 0.719
99 Q 1.000** 4.758 +- 0.587
100 A 1.000** 4.758 +- 0.585
106 T 0.790 3.896 +- 1.651
107 Y 0.821 4.020 +- 1.557
113 G 0.808 3.961 +- 1.578
114 V 0.979* 4.674 +- 0.802
115 V 1.000** 4.758 +- 0.585
119 T 0.725 3.635 +- 1.829
133 S 0.935 4.497 +- 1.114
149 S 0.924 4.448 +- 1.166
178 Q 0.814 3.985 +- 1.563
195 R 0.690 3.487 +- 1.823
257 S 0.995** 4.738 +- 0.648
258 G 0.928 4.471 +- 1.151
262 T 0.760 3.780 +- 1.762
263 G 0.696 3.520 +- 1.880
