--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Apr 12 00:52:40 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-DRB5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB5/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 -2070.09 -2086.67
2 -2070.24 -2083.84
--------------------------------------
TOTAL -2070.16 -2086.03
--------------------------------------
Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DRB5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB5/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} 0.387002 0.002772 0.302000 0.506000 0.381000 1.002
r(A<->C){all} 0.063303 0.000621 0.021490 0.117950 0.060938 1.000
r(A<->G){all} 0.298973 0.001963 0.216633 0.390808 0.297989 1.000
r(A<->T){all} 0.103916 0.001019 0.049369 0.171716 0.101087 1.001
r(C<->G){all} 0.097919 0.000523 0.057623 0.147252 0.096397 1.000
r(C<->T){all} 0.366160 0.002758 0.268401 0.474117 0.364419 1.000
r(G<->T){all} 0.069729 0.000452 0.033963 0.117084 0.067622 1.000
pi(A){all} 0.223771 0.000189 0.197390 0.251420 0.223506 1.000
pi(C){all} 0.252485 0.000208 0.224846 0.281379 0.252357 1.000
pi(G){all} 0.319789 0.000228 0.290485 0.349826 0.319538 1.000
pi(T){all} 0.203956 0.000181 0.178250 0.231141 0.203611 1.000
alpha{1,2} 28.031627 2721.559097 0.308864 180.764229 1.105597 1.012
alpha{3} 101.990667 3266.394053 6.809541 195.003643 100.976671 1.000
pinvar{all} 0.607037 0.006145 0.427042 0.720997 0.620129 1.007
---------------------------------------------------------------------------------------------
* 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 -2002.415363
Model 7: beta -2013.086717
Model 1: NearlyNeutral -2012.263927
Model 2: PositiveSelection -2002.425163
Model 2 vs 1 19.67752799999971
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_002116.2_HLA-DRB5)
Pr(w>1) post mean +- SE for w
3 C 0.593 3.085
14 K 0.962* 4.446
38 Q 0.647 3.312
42 Y 0.929 4.329
55 F 0.963* 4.451
59 D 0.885 4.171
66 D 0.730 3.610
67 L 0.847 4.030
95 F 0.961* 4.442
98 D 0.992** 4.554
99 R 0.641 3.255
102 A 0.727 3.599
106 Y 0.939 4.363
114 G 0.961* 4.442
118 T 0.733 3.607
124 E 0.906 4.248
185 T 0.580 3.035
243 A 0.786 3.812
259 H 0.536 2.870
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_002116.2_HLA-DRB5)
Pr(w>1) post mean +- SE for w
14 K 0.939 5.211 +- 2.037
38 Q 0.517 2.982 +- 2.230
42 Y 0.897 5.014 +- 2.172
55 F 0.949 5.278 +- 2.013
59 D 0.787 4.346 +- 2.291
66 D 0.595 3.358 +- 2.306
67 L 0.798 4.527 +- 2.395
95 F 0.943 5.246 +- 2.030
98 D 0.989* 5.475 +- 1.846
99 R 0.530 3.083 +- 2.368
102 A 0.595 3.367 +- 2.316
106 Y 0.897 4.986 +- 2.148
114 G 0.941 5.235 +- 2.035
118 T 0.629 3.585 +- 2.429
124 E 0.821 4.530 +- 2.253
243 A 0.662 3.705 +- 2.351
Model 8 vs 7 21.342707999999675
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_002116.2_HLA-DRB5)
Pr(w>1) post mean +- SE for w
3 C 0.661 3.108
14 K 0.985* 4.340
38 Q 0.757 3.486
40 D 0.534 2.622
42 Y 0.963* 4.256
55 F 0.985* 4.339
59 D 0.951* 4.212
66 D 0.828 3.750
67 L 0.901 4.022
95 F 0.984* 4.336
98 D 0.997** 4.384
99 R 0.692 3.221
102 A 0.825 3.740
106 Y 0.971* 4.287
114 G 0.985* 4.337
118 T 0.797 3.625
124 E 0.962* 4.252
185 T 0.644 3.043
243 A 0.871 3.914
259 H 0.603 2.885
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_002116.2_HLA-DRB5)
Pr(w>1) post mean +- SE for w
3 C 0.571 2.856 +- 2.258
14 K 0.975* 4.930 +- 1.855
38 Q 0.640 3.168 +- 2.234
42 Y 0.946 4.797 +- 1.964
55 F 0.978* 4.949 +- 1.848
59 D 0.898 4.509 +- 2.057
66 D 0.719 3.569 +- 2.253
67 L 0.870 4.438 +- 2.183
95 F 0.976* 4.937 +- 1.855
98 D 0.996** 5.032 +- 1.772
99 R 0.608 3.059 +- 2.323
102 A 0.719 3.575 +- 2.260
106 Y 0.952* 4.813 +- 1.935
114 G 0.975* 4.934 +- 1.856
118 T 0.720 3.625 +- 2.337
124 E 0.919 4.623 +- 2.009
185 T 0.563 2.833 +- 2.273
243 A 0.782 3.905 +- 2.236
259 H 0.517 2.586 +- 2.178
