--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 16:20:23 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-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-A/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 -5909.40 -5935.27
2 -5909.37 -5931.65
--------------------------------------
TOTAL -5909.38 -5934.61
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-A/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} 1.109961 0.003825 0.994000 1.239000 1.108000 1.000
r(A<->C){all} 0.095601 0.000166 0.072136 0.122642 0.095061 1.000
r(A<->G){all} 0.279253 0.000490 0.238371 0.324604 0.278602 1.001
r(A<->T){all} 0.193750 0.000547 0.150107 0.240722 0.192812 1.000
r(C<->G){all} 0.091954 0.000101 0.073221 0.112563 0.091674 1.000
r(C<->T){all} 0.257683 0.000498 0.216122 0.302160 0.257316 1.000
r(G<->T){all} 0.081758 0.000149 0.059002 0.107330 0.081475 1.000
pi(A){all} 0.202443 0.000118 0.181573 0.224377 0.202373 1.002
pi(C){all} 0.298799 0.000149 0.274967 0.323140 0.298940 1.001
pi(G){all} 0.329078 0.000162 0.304693 0.354435 0.329070 1.000
pi(T){all} 0.169681 0.000106 0.149769 0.190551 0.169556 1.000
alpha{1,2} 0.472662 0.008433 0.318552 0.679073 0.463913 1.001
alpha{3} 29.894653 2476.758009 1.391730 178.022267 4.640338 1.005
pinvar{all} 0.312287 0.003464 0.183530 0.408660 0.318791 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 -5759.42454
Model 7: beta -5841.633019
Model 1: NearlyNeutral -5834.894205
Model 2: PositiveSelection -5761.132259
Model 2 vs 1 147.52389199999925
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_002107.3_HLA-A)
Pr(w>1) post mean +- SE for w
30 F 0.986* 5.076
45 A 0.999** 5.131
83 Q 0.780 4.225
84 E 0.988* 5.086
87 N 1.000** 5.134
88 V 0.934 4.861
94 T 0.970* 5.012
98 D 0.999** 5.132
118 I 1.000** 5.134
135 R 1.000** 5.134
137 D 0.999** 5.130
172 H 0.998** 5.128
173 E 0.997** 5.120
177 L 1.000** 5.134
184 T 1.000** 5.134
318 T 0.833 4.443
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_002107.3_HLA-A)
Pr(w>1) post mean +- SE for w
30 F 0.987* 5.061 +- 0.722
45 A 0.999** 5.113 +- 0.569
83 Q 0.798 4.241 +- 1.699
84 E 0.990* 5.073 +- 0.691
87 N 1.000** 5.116 +- 0.559
88 V 0.942 4.868 +- 1.102
94 T 0.974* 5.008 +- 0.853
98 D 0.999** 5.113 +- 0.567
118 I 1.000** 5.116 +- 0.558
135 R 1.000** 5.116 +- 0.558
137 D 0.999** 5.112 +- 0.572
172 H 0.999** 5.110 +- 0.579
173 E 0.997** 5.104 +- 0.600
177 L 1.000** 5.116 +- 0.558
184 T 1.000** 5.115 +- 0.560
316 A 0.548 3.221 +- 2.060
318 T 0.854 4.505 +- 1.536
Model 8 vs 7 164.4169579999998
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_002107.3_HLA-A)
Pr(w>1) post mean +- SE for w
30 F 0.994** 4.532
45 A 1.000** 4.552
83 Q 0.901 4.192
84 E 0.995** 4.535
87 N 1.000** 4.554
88 V 0.970* 4.444
91 Q 0.548 2.898
94 T 0.986* 4.501
98 D 1.000** 4.553
118 I 1.000** 4.554
135 R 1.000** 4.554
137 D 1.000** 4.552
172 H 0.999** 4.551
173 E 0.998** 4.548
177 L 1.000** 4.554
184 T 1.000** 4.554
316 A 0.639 3.209
318 T 0.906 4.205
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_002107.3_HLA-A)
Pr(w>1) post mean +- SE for w
30 F 0.993** 4.606 +- 0.500
45 A 1.000** 4.631 +- 0.406
83 Q 0.883 4.176 +- 1.247
84 E 0.994** 4.611 +- 0.484
87 N 1.000** 4.632 +- 0.399
88 V 0.967* 4.505 +- 0.775
91 Q 0.518 2.781 +- 1.846
94 T 0.984* 4.573 +- 0.610
98 D 1.000** 4.631 +- 0.404
118 I 1.000** 4.632 +- 0.398
135 R 1.000** 4.632 +- 0.399
137 D 0.999** 4.630 +- 0.407
172 H 0.999** 4.629 +- 0.413
173 E 0.998** 4.626 +- 0.426
177 L 1.000** 4.632 +- 0.398
184 T 1.000** 4.632 +- 0.400
316 A 0.617 3.159 +- 1.865
318 T 0.898 4.243 +- 1.203
