--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Apr 12 01:12:45 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-E/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-E/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 -3585.38 -3603.86
2 -3585.34 -3604.67
--------------------------------------
TOTAL -3585.36 -3604.35
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-E/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-E/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} 0.454646 0.001094 0.394000 0.523000 0.453000 1.002
r(A<->C){all} 0.091623 0.000340 0.058053 0.130208 0.090736 1.001
r(A<->G){all} 0.280642 0.000929 0.223083 0.342813 0.279684 1.000
r(A<->T){all} 0.146965 0.000896 0.092771 0.209560 0.145327 1.001
r(C<->G){all} 0.089806 0.000197 0.064316 0.119526 0.089177 1.001
r(C<->T){all} 0.284039 0.000995 0.225588 0.348399 0.283189 1.000
r(G<->T){all} 0.106925 0.000373 0.072371 0.146891 0.105936 1.000
pi(A){all} 0.205018 0.000121 0.183878 0.227103 0.204839 1.000
pi(C){all} 0.294485 0.000152 0.270514 0.318932 0.294500 1.001
pi(G){all} 0.320964 0.000169 0.295663 0.346301 0.320992 1.000
pi(T){all} 0.179533 0.000108 0.160089 0.200524 0.179376 1.001
alpha{1,2} 0.878805 18.509750 0.314995 1.745207 0.625052 1.000
alpha{3} 96.624216 3406.951439 4.913938 194.573897 95.143201 1.000
pinvar{all} 0.419255 0.005973 0.250433 0.552914 0.425489 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 -2996.868094
Model 7: beta -3011.491184
Model 1: NearlyNeutral -3008.561247
Model 2: PositiveSelection -2996.000173
Model 2 vs 1 25.12214800000038
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_005507.3_HLA-E)
Pr(w>1) post mean +- SE for w
2 V 0.976* 6.438
3 D 0.937 6.218
4 G 0.977* 6.441
96 R 0.790 5.399
162 Q 0.646 4.596
168 S 0.998** 6.560
187 K 0.663 4.691
200 E 0.697 4.879
305 I 0.526 3.932
306 A 0.642 4.573
309 V 0.720 5.008
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_005507.3_HLA-E)
Pr(w>1) post mean +- SE for w
2 V 0.976* 6.720 +- 1.869
3 D 0.937 6.513 +- 2.145
4 G 0.975* 6.722 +- 1.875
96 R 0.768 5.351 +- 2.768
162 Q 0.653 4.807 +- 3.075
168 S 0.998** 6.837 +- 1.682
187 K 0.659 4.793 +- 3.027
200 E 0.675 4.799 +- 2.936
305 I 0.520 3.914 +- 3.023
306 A 0.640 4.678 +- 3.048
309 V 0.720 5.181 +- 2.954
Model 8 vs 7 29.246180000000095
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_005507.3_HLA-E)
Pr(w>1) post mean +- SE for w
2 V 0.985* 5.929
3 D 0.955* 5.779
4 G 0.982* 5.916
96 R 0.888 5.435
162 Q 0.721 4.576
168 S 0.999** 6.000
187 K 0.750 4.725
200 E 0.809 5.032
305 I 0.639 4.155
306 A 0.731 4.630
309 V 0.793 4.946
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_005507.3_HLA-E)
Pr(w>1) post mean +- SE for w
2 V 0.988* 5.355 +- 1.456
3 D 0.965* 5.262 +- 1.590
4 G 0.983* 5.339 +- 1.486
96 R 0.934 5.075 +- 1.721
162 Q 0.803 4.515 +- 2.196
168 S 0.999** 5.399 +- 1.388
187 K 0.829 4.615 +- 2.115
198 H 0.526 3.045 +- 2.240
200 E 0.878 4.815 +- 1.937
305 I 0.751 4.223 +- 2.264
306 A 0.816 4.554 +- 2.148
309 V 0.857 4.758 +- 2.038
