--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 21:27:29 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-DPB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/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 -4411.57 -4439.47
2 -4412.00 -4437.69
--------------------------------------
TOTAL -4411.76 -4438.94
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DPB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/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} 1.311948 0.007611 1.153000 1.496000 1.307000 1.000
r(A<->C){all} 0.095493 0.000219 0.068544 0.126381 0.094675 1.000
r(A<->G){all} 0.251606 0.000629 0.204519 0.302783 0.250939 1.000
r(A<->T){all} 0.131658 0.000404 0.094393 0.173911 0.130884 1.002
r(C<->G){all} 0.088068 0.000142 0.066288 0.113269 0.087352 1.001
r(C<->T){all} 0.352732 0.000880 0.295231 0.410377 0.352657 1.000
r(G<->T){all} 0.080443 0.000174 0.056402 0.108313 0.079709 1.001
pi(A){all} 0.225367 0.000179 0.199610 0.252287 0.225029 1.000
pi(C){all} 0.274419 0.000199 0.247549 0.302189 0.274053 1.000
pi(G){all} 0.317525 0.000211 0.289375 0.346309 0.317246 1.000
pi(T){all} 0.182689 0.000147 0.159618 0.207011 0.182315 1.000
alpha{1,2} 0.401000 0.005573 0.282508 0.577192 0.391201 1.000
alpha{3} 4.420312 207.782930 1.028336 16.983666 2.132486 1.004
pinvar{all} 0.234107 0.003978 0.100442 0.346728 0.237641 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 -4296.78762
Model 7: beta -4339.577445
Model 1: NearlyNeutral -4331.797585
Model 2: PositiveSelection -4297.35627
Model 2 vs 1 68.88263000000006
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_002112.3_HLA-DPB1)
Pr(w>1) post mean +- SE for w
10 R 0.760 3.586
24 S 0.531 2.809
37 F 0.658 3.239
39 G 1.000** 4.405
41 Q 0.984* 4.349
63 F 0.902 4.071
83 A 1.000** 4.404
90 I 1.000** 4.405
93 E 0.952* 4.240
254 A 0.976* 4.323
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_002112.3_HLA-DPB1)
Pr(w>1) post mean +- SE for w
10 R 0.704 3.190 +- 1.556
24 S 0.567 2.839 +- 1.768
37 F 0.640 2.973 +- 1.600
39 G 1.000** 4.552 +- 1.223
41 Q 0.976* 4.431 +- 1.271
63 F 0.848 3.796 +- 1.455
83 A 1.000** 4.551 +- 1.224
90 I 1.000** 4.552 +- 1.223
93 E 0.915 4.107 +- 1.358
254 A 0.975* 4.449 +- 1.310
Model 8 vs 7 85.57964999999967
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_002112.3_HLA-DPB1)
Pr(w>1) post mean +- SE for w
7 A 0.658 2.290
8 A 0.899 2.849
10 R 0.990* 3.055
15 T 0.745 2.498
24 S 0.866 2.766
36 L 0.935 2.931
37 F 0.978* 3.029
39 G 1.000** 3.078
41 Q 0.999** 3.075
46 F 0.705 2.387
52 F 0.531 1.995
63 F 0.995** 3.067
64 A 0.890 2.829
83 A 1.000** 3.078
90 I 1.000** 3.078
93 E 0.998** 3.073
94 K 0.897 2.844
97 V 0.805 2.634
117 R 0.667 2.287
254 A 0.996** 3.069
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_002112.3_HLA-DPB1)
Pr(w>1) post mean +- SE for w
8 A 0.678 2.535 +- 1.239
10 R 0.955* 3.371 +- 0.829
24 S 0.771 2.847 +- 1.251
36 L 0.793 2.882 +- 1.163
37 F 0.921 3.267 +- 0.932
39 G 1.000** 3.511 +- 0.664
41 Q 0.996** 3.501 +- 0.681
46 F 0.520 2.100 +- 1.322
63 F 0.982* 3.456 +- 0.739
64 A 0.712 2.652 +- 1.248
83 A 1.000** 3.511 +- 0.665
90 I 1.000** 3.511 +- 0.664
93 E 0.991** 3.485 +- 0.701
94 K 0.677 2.536 +- 1.242
97 V 0.541 2.151 +- 1.257
117 R 0.520 2.105 +- 1.364
254 A 0.992** 3.489 +- 0.702
