--- 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