--- 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