--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 16:37:27 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-B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-B/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 -4171.12 -4188.03
2 -4171.16 -4187.07
--------------------------------------
TOTAL -4171.14 -4187.66
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-B/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} 0.627749 0.001702 0.550000 0.712000 0.626000 1.001
r(A<->C){all} 0.134005 0.000360 0.098782 0.172906 0.133211 1.003
r(A<->G){all} 0.284803 0.000745 0.234453 0.340036 0.284435 1.000
r(A<->T){all} 0.154298 0.000751 0.103732 0.210782 0.153062 1.000
r(C<->G){all} 0.100612 0.000168 0.076849 0.127632 0.100068 1.000
r(C<->T){all} 0.219640 0.000647 0.172784 0.272735 0.218589 1.001
r(G<->T){all} 0.106642 0.000313 0.073956 0.143659 0.105904 1.000
pi(A){all} 0.191798 0.000101 0.172470 0.212256 0.191536 1.001
pi(C){all} 0.301237 0.000141 0.278043 0.324580 0.301377 1.000
pi(G){all} 0.336693 0.000151 0.312950 0.361432 0.336605 1.000
pi(T){all} 0.170273 0.000096 0.151698 0.189763 0.170126 1.000
alpha{1,2} 0.598254 0.025826 0.360302 0.978416 0.573430 1.000
alpha{3} 90.738893 3641.074553 3.122157 194.189996 87.289994 1.001
pinvar{all} 0.381108 0.003557 0.250192 0.484477 0.385870 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 -3732.040354
Model 7: beta -3775.537668
Model 1: NearlyNeutral -3766.262518
Model 2: PositiveSelection -3732.126421
Model 2 vs 1 68.27219400000013
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_005505.2_HLA-B)
Pr(w>1) post mean +- SE for w
30 Y 0.978* 4.153
32 S 0.534 2.722
45 S 0.863 3.782
66 E 0.935 4.015
73 I 0.935 4.017
84 N 0.948 4.056
87 I 0.978* 4.155
88 Y 0.962* 4.104
90 A 0.725 3.339
91 Q 0.987* 4.184
92 A 0.591 2.878
95 D 0.970* 4.127
98 S 0.797 3.572
101 N 0.580 2.871
116 L 0.874 3.818
118 S 0.933 4.011
135 D 1.000** 4.224
137 Y 0.584 2.883
173 E 0.997** 4.214
177 R 0.999** 4.223
184 E 1.000** 4.224
257 A 0.627 2.998
325 S 0.711 3.277
333 S 0.614 2.953
337 C 0.997** 4.216
340 S 0.688 3.216
341 A 0.591 2.906
344 S 0.590 2.875
347 S 0.627 2.996
350 A 0.960* 4.098
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_005505.2_HLA-B)
Pr(w>1) post mean +- SE for w
30 Y 0.979* 4.068 +- 0.824
32 S 0.596 2.770 +- 1.546
45 S 0.876 3.716 +- 1.210
66 E 0.938 3.923 +- 1.005
73 I 0.943 3.948 +- 0.993
84 N 0.953* 3.978 +- 0.950
87 I 0.980* 4.074 +- 0.818
88 Y 0.966* 4.024 +- 0.891
90 A 0.759 3.316 +- 1.430
91 Q 0.988* 4.100 +- 0.774
92 A 0.631 2.872 +- 1.620
95 D 0.972* 4.045 +- 0.860
97 E 0.519 2.507 +- 1.522
98 S 0.818 3.507 +- 1.330
101 N 0.634 2.880 +- 1.514
116 L 0.885 3.740 +- 1.182
118 S 0.939 3.930 +- 1.005
135 D 1.000** 4.138 +- 0.704
137 Y 0.635 2.886 +- 1.519
173 E 0.997** 4.130 +- 0.721
177 R 0.999** 4.137 +- 0.706
184 E 1.000** 4.138 +- 0.703
257 A 0.663 2.986 +- 1.600
325 S 0.740 3.254 +- 1.523
333 S 0.651 2.942 +- 1.607
335 A 0.541 2.559 +- 1.634
337 C 0.997** 4.130 +- 0.719
340 S 0.724 3.199 +- 1.489
341 A 0.641 2.898 +- 1.510
344 S 0.630 2.868 +- 1.619
347 S 0.663 2.983 +- 1.599
350 A 0.965* 4.026 +- 0.898
Model 8 vs 7 86.99462799999947
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_005505.2_HLA-B)
Pr(w>1) post mean +- SE for w
30 Y 0.996** 3.827
32 S 0.749 3.054
45 S 0.947 3.674
66 E 0.986* 3.796
73 I 0.982* 3.785
84 N 0.989* 3.806
87 I 0.996** 3.826
88 Y 0.991** 3.813
90 A 0.897 3.520
91 Q 0.998** 3.833
92 A 0.702 2.883
95 D 0.993** 3.819
97 E 0.698 2.897
98 S 0.943 3.664
101 N 0.830 3.312
116 L 0.961* 3.719
118 S 0.984* 3.791
124 V 0.662 2.782
135 D 1.000** 3.839
137 Y 0.806 3.233
142 K 0.604 2.601
152 R 0.605 2.601
173 E 0.999** 3.838
177 R 1.000** 3.839
184 E 1.000** 3.839
257 A 0.732 2.980
325 S 0.800 3.200
333 S 0.722 2.947
335 A 0.614 2.599
337 C 0.999** 3.838
340 S 0.829 3.302
341 A 0.824 3.292
344 S 0.702 2.883
347 S 0.733 2.984
350 A 0.986* 3.795
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_005505.2_HLA-B)
Pr(w>1) post mean +- SE for w
30 Y 0.996** 3.579 +- 0.394
32 S 0.829 3.077 +- 1.109
45 S 0.962* 3.474 +- 0.644
66 E 0.989* 3.556 +- 0.457
73 I 0.986* 3.549 +- 0.480
84 N 0.991** 3.563 +- 0.439
87 I 0.996** 3.579 +- 0.395
88 Y 0.993** 3.569 +- 0.425
90 A 0.928 3.375 +- 0.794
91 Q 0.998** 3.584 +- 0.380
92 A 0.781 2.927 +- 1.255
95 D 0.994** 3.573 +- 0.413
97 E 0.798 2.985 +- 1.166
98 S 0.959* 3.466 +- 0.645
101 N 0.886 3.246 +- 0.939
111 A 0.560 2.272 +- 1.458
116 L 0.972* 3.504 +- 0.580
118 S 0.988* 3.553 +- 0.467
124 V 0.772 2.907 +- 1.219
134 H 0.535 2.176 +- 1.497
135 D 1.000** 3.589 +- 0.362
137 Y 0.869 3.194 +- 1.000
142 K 0.738 2.804 +- 1.263
152 R 0.732 2.789 +- 1.280
173 E 0.999** 3.587 +- 0.367
177 R 1.000** 3.589 +- 0.363
184 E 1.000** 3.589 +- 0.362
188 W 0.556 2.258 +- 1.446
257 A 0.804 2.995 +- 1.211
325 S 0.853 3.146 +- 1.092
333 S 0.796 2.972 +- 1.225
335 A 0.716 2.725 +- 1.360
337 C 0.999** 3.588 +- 0.366
340 S 0.880 3.229 +- 0.986
341 A 0.882 3.231 +- 0.957
344 S 0.782 2.927 +- 1.255
347 S 0.805 2.998 +- 1.208
350 A 0.989* 3.557 +- 0.465
