--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Apr 12 00:46:37 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-DRB3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB3/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 -1980.50 -1997.15
2 -1980.38 -1998.75
--------------------------------------
TOTAL -1980.44 -1998.24
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DRB3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB3/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} 0.265317 0.000885 0.212000 0.329000 0.263000 1.000
r(A<->C){all} 0.101350 0.000840 0.051181 0.164004 0.098791 1.000
r(A<->G){all} 0.168862 0.001157 0.109084 0.242242 0.166530 1.000
r(A<->T){all} 0.210862 0.002079 0.129527 0.306510 0.208112 1.000
r(C<->G){all} 0.094341 0.000483 0.056313 0.141940 0.092704 1.000
r(C<->T){all} 0.340278 0.002551 0.245988 0.442625 0.338700 1.000
r(G<->T){all} 0.084306 0.000597 0.042649 0.137257 0.082479 1.002
pi(A){all} 0.216659 0.000197 0.189988 0.244904 0.216516 1.000
pi(C){all} 0.261869 0.000218 0.233643 0.291465 0.261522 1.000
pi(G){all} 0.316085 0.000245 0.286490 0.346889 0.315873 1.000
pi(T){all} 0.205388 0.000185 0.179485 0.232576 0.205199 1.000
alpha{1,2} 28.084679 2735.050281 0.173688 179.276444 0.846342 1.003
alpha{3} 100.482318 3261.914324 7.034359 194.807984 99.861952 1.000
pinvar{all} 0.694802 0.009037 0.471945 0.815786 0.712470 1.003
---------------------------------------------------------------------------------------------
* 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 -1807.692703
Model 7: beta -1836.888718
Model 1: NearlyNeutral -1836.836979
Model 2: PositiveSelection -1807.692074
Model 2 vs 1 58.28980999999976
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_072049.2_HLA-DRB3)
Pr(w>1) post mean +- SE for w
28 L 0.954* 7.852
29 R 1.000** 8.181
31 S 0.803 6.768
46 D 0.973* 7.987
50 H 0.682 5.897
55 F 1.000** 8.179
56 L 0.549 4.940
75 V 0.999** 8.175
85 L 1.000** 8.181
92 R 0.931 7.686
104 G 0.953* 7.841
122 A 0.773 6.548
138 S 0.925 7.641
205 E 0.585 5.201
245 H 0.720 6.169
246 S 0.963* 7.915
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_072049.2_HLA-DRB3)
Pr(w>1) post mean +- SE for w
28 L 0.957* 7.475 +- 2.185
29 R 1.000** 7.800 +- 1.733
31 S 0.823 6.506 +- 3.010
46 D 0.974* 7.601 +- 2.024
50 H 0.717 5.702 +- 3.311
55 F 1.000** 7.799 +- 1.736
56 L 0.609 4.832 +- 3.349
75 V 0.999** 7.794 +- 1.744
85 L 1.000** 7.800 +- 1.733
92 R 0.935 7.304 +- 2.363
104 G 0.957* 7.489 +- 2.189
122 A 0.796 6.305 +- 3.109
138 S 0.931 7.297 +- 2.396
205 E 0.635 5.080 +- 3.402
245 H 0.747 5.870 +- 3.203
246 S 0.966* 7.559 +- 2.107
Model 8 vs 7 58.39202999999998
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_072049.2_HLA-DRB3)
Pr(w>1) post mean +- SE for w
28 L 0.955* 7.817
29 R 1.000** 8.141
31 S 0.805 6.746
46 D 0.973* 7.950
50 H 0.684 5.888
55 F 1.000** 8.139
56 L 0.553 4.948
75 V 0.999** 8.135
85 L 1.000** 8.141
92 R 0.932 7.654
104 G 0.953* 7.805
122 A 0.774 6.530
138 S 0.925 7.608
205 E 0.588 5.202
245 H 0.723 6.162
246 S 0.963* 7.878
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_072049.2_HLA-DRB3)
Pr(w>1) post mean +- SE for w
14 R 0.607 3.608 +- 2.669
18 A 0.521 3.120 +- 2.659
22 R 0.648 3.846 +- 2.652
23 P 0.604 3.590 +- 2.670
24 R 0.529 3.168 +- 2.663
28 L 0.992** 5.888 +- 1.485
29 R 1.000** 5.940 +- 1.431
31 S 0.939 5.562 +- 1.817
44 Y 0.749 4.364 +- 2.329
46 D 0.996** 5.914 +- 1.457
50 H 0.903 5.322 +- 1.965
55 F 1.000** 5.940 +- 1.431
56 L 0.898 5.246 +- 1.910
75 V 1.000** 5.939 +- 1.432
78 S 0.781 4.551 +- 2.275
85 L 1.000** 5.940 +- 1.431
86 L 0.735 4.283 +- 2.352
88 Q 0.590 3.478 +- 2.465
89 K 0.523 3.121 +- 2.458
92 R 0.988* 5.861 +- 1.508
99 H 0.630 3.693 +- 2.452
102 G 0.549 3.261 +- 2.470
104 G 0.989* 5.872 +- 1.515
122 A 0.930 5.502 +- 1.859
131 N 0.645 3.773 +- 2.441
138 S 0.983* 5.833 +- 1.552
153 G 0.668 3.903 +- 2.424
184 R 0.678 3.966 +- 2.425
201 A 0.569 3.394 +- 2.672
205 E 0.872 5.120 +- 2.066
209 R 0.725 4.225 +- 2.361
245 H 0.940 5.531 +- 1.756
246 S 0.990* 5.879 +- 1.512
247 G 0.704 4.159 +- 2.574
