--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Apr 11 16:41:35 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-C/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-C/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 -2201.93 -2212.00
2 -2201.72 -2211.50
--------------------------------------
TOTAL -2201.82 -2211.78
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-C/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-C/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} 0.153378 0.000348 0.121000 0.194000 0.152000 1.000
r(A<->C){all} 0.174749 0.001467 0.107554 0.255721 0.172343 1.000
r(A<->G){all} 0.324630 0.002602 0.230865 0.431846 0.322444 1.001
r(A<->T){all} 0.093258 0.001647 0.026583 0.182979 0.089277 1.000
r(C<->G){all} 0.066932 0.000408 0.032570 0.111913 0.065296 1.001
r(C<->T){all} 0.248857 0.002409 0.160052 0.351556 0.245570 1.000
r(G<->T){all} 0.091573 0.000899 0.041045 0.157659 0.088704 1.000
pi(A){all} 0.198705 0.000134 0.176542 0.221935 0.198423 1.000
pi(C){all} 0.308291 0.000181 0.282091 0.334931 0.308300 1.000
pi(G){all} 0.336199 0.000192 0.309184 0.363398 0.336024 1.000
pi(T){all} 0.156804 0.000112 0.136500 0.178466 0.156590 1.000
alpha{1,2} 82.406501 4003.004596 0.372055 193.337012 77.504659 1.002
alpha{3} 103.533438 3171.092922 9.735424 195.283904 103.721452 1.001
pinvar{all} 0.777500 0.003801 0.615880 0.847185 0.790397 1.002
---------------------------------------------------------------------------------------------
* 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 -2152.118753
Model 7: beta -2165.809291
Model 1: NearlyNeutral -2165.808156
Model 2: PositiveSelection -2152.140463
Model 2 vs 1 27.335385999999744
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_002108.4_HLA-C)
Pr(w>1) post mean +- SE for w
48 S 0.866 10.052
97 A 0.983* 11.280
104 N 0.548 6.705
121 R 0.995** 11.403
138 D 0.938 10.809
140 S 0.860 9.993
171 L 0.574 6.984
180 L 0.989* 11.342
187 T 0.991** 11.360
329 A 0.813 9.495
362 T 0.814 9.500
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_002108.4_HLA-C)
Pr(w>1) post mean +- SE for w
48 S 0.866 7.729 +- 3.045
97 A 0.980* 8.636 +- 1.860
104 N 0.622 5.727 +- 4.002
121 R 0.994** 8.743 +- 1.630
138 D 0.958* 8.451 +- 2.159
140 S 0.899 7.980 +- 2.759
171 L 0.671 6.115 +- 3.892
180 L 0.987* 8.692 +- 1.744
187 T 0.991** 8.719 +- 1.683
329 A 0.828 7.418 +- 3.289
362 T 0.829 7.426 +- 3.283
Model 8 vs 7 27.381075999999666
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_002108.4_HLA-C)
Pr(w>1) post mean +- SE for w
48 S 0.874 10.006
97 A 0.986* 11.184
104 N 0.558 6.679
121 R 0.996** 11.290
138 D 0.954* 10.844
140 S 0.882 10.092
171 L 0.590 7.019
180 L 0.991** 11.236
187 T 0.993** 11.259
329 A 0.823 9.473
362 T 0.824 9.479
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_002108.4_HLA-C)
Pr(w>1) post mean +- SE for w
48 S 0.898 8.060 +- 2.808
97 A 0.989* 8.782 +- 1.631
104 N 0.669 6.157 +- 4.030
121 R 0.997** 8.849 +- 1.456
138 D 0.980* 8.706 +- 1.789
140 S 0.938 8.366 +- 2.382
171 L 0.723 6.590 +- 3.851
180 L 0.993** 8.815 +- 1.548
187 T 0.996** 8.838 +- 1.485
208 P 0.542 5.065 +- 4.181
329 A 0.867 7.800 +- 3.074
362 T 0.868 7.807 +- 3.066
