--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 16:20:23 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-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-A/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       -5909.40          -5935.27
2       -5909.37          -5931.65
--------------------------------------
TOTAL     -5909.38          -5934.61
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-A/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}           1.109961      0.003825      0.994000      1.239000      1.108000      1.000
r(A<->C){all}     0.095601      0.000166      0.072136      0.122642      0.095061      1.000
r(A<->G){all}     0.279253      0.000490      0.238371      0.324604      0.278602      1.001
r(A<->T){all}     0.193750      0.000547      0.150107      0.240722      0.192812      1.000
r(C<->G){all}     0.091954      0.000101      0.073221      0.112563      0.091674      1.000
r(C<->T){all}     0.257683      0.000498      0.216122      0.302160      0.257316      1.000
r(G<->T){all}     0.081758      0.000149      0.059002      0.107330      0.081475      1.000
pi(A){all}        0.202443      0.000118      0.181573      0.224377      0.202373      1.002
pi(C){all}        0.298799      0.000149      0.274967      0.323140      0.298940      1.001
pi(G){all}        0.329078      0.000162      0.304693      0.354435      0.329070      1.000
pi(T){all}        0.169681      0.000106      0.149769      0.190551      0.169556      1.000
alpha{1,2}        0.472662      0.008433      0.318552      0.679073      0.463913      1.001
alpha{3}         29.894653   2476.758009      1.391730    178.022267      4.640338      1.005
pinvar{all}       0.312287      0.003464      0.183530      0.408660      0.318791      1.001
---------------------------------------------------------------------------------------------
* 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	-5759.42454
Model 7: beta	-5841.633019
Model 1: NearlyNeutral	-5834.894205
Model 2: PositiveSelection	-5761.132259


Model 2 vs 1	147.52389199999925

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_002107.3_HLA-A)

            Pr(w>1)     post mean +- SE for w

    30 F      0.986*        5.076
    45 A      0.999**       5.131
    83 Q      0.780         4.225
    84 E      0.988*        5.086
    87 N      1.000**       5.134
    88 V      0.934         4.861
    94 T      0.970*        5.012
    98 D      0.999**       5.132
   118 I      1.000**       5.134
   135 R      1.000**       5.134
   137 D      0.999**       5.130
   172 H      0.998**       5.128
   173 E      0.997**       5.120
   177 L      1.000**       5.134
   184 T      1.000**       5.134
   318 T      0.833         4.443

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_002107.3_HLA-A)

            Pr(w>1)     post mean +- SE for w

    30 F      0.987*        5.061 +- 0.722
    45 A      0.999**       5.113 +- 0.569
    83 Q      0.798         4.241 +- 1.699
    84 E      0.990*        5.073 +- 0.691
    87 N      1.000**       5.116 +- 0.559
    88 V      0.942         4.868 +- 1.102
    94 T      0.974*        5.008 +- 0.853
    98 D      0.999**       5.113 +- 0.567
   118 I      1.000**       5.116 +- 0.558
   135 R      1.000**       5.116 +- 0.558
   137 D      0.999**       5.112 +- 0.572
   172 H      0.999**       5.110 +- 0.579
   173 E      0.997**       5.104 +- 0.600
   177 L      1.000**       5.116 +- 0.558
   184 T      1.000**       5.115 +- 0.560
   316 A      0.548         3.221 +- 2.060
   318 T      0.854         4.505 +- 1.536


Model 8 vs 7	164.4169579999998

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_002107.3_HLA-A)

            Pr(w>1)     post mean +- SE for w

    30 F      0.994**       4.532
    45 A      1.000**       4.552
    83 Q      0.901         4.192
    84 E      0.995**       4.535
    87 N      1.000**       4.554
    88 V      0.970*        4.444
    91 Q      0.548         2.898
    94 T      0.986*        4.501
    98 D      1.000**       4.553
   118 I      1.000**       4.554
   135 R      1.000**       4.554
   137 D      1.000**       4.552
   172 H      0.999**       4.551
   173 E      0.998**       4.548
   177 L      1.000**       4.554
   184 T      1.000**       4.554
   316 A      0.639         3.209
   318 T      0.906         4.205

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_002107.3_HLA-A)

            Pr(w>1)     post mean +- SE for w

    30 F      0.993**       4.606 +- 0.500
    45 A      1.000**       4.631 +- 0.406
    83 Q      0.883         4.176 +- 1.247
    84 E      0.994**       4.611 +- 0.484
    87 N      1.000**       4.632 +- 0.399
    88 V      0.967*        4.505 +- 0.775
    91 Q      0.518         2.781 +- 1.846
    94 T      0.984*        4.573 +- 0.610
    98 D      1.000**       4.631 +- 0.404
   118 I      1.000**       4.632 +- 0.398
   135 R      1.000**       4.632 +- 0.399
   137 D      0.999**       4.630 +- 0.407
   172 H      0.999**       4.629 +- 0.413
   173 E      0.998**       4.626 +- 0.426
   177 L      1.000**       4.632 +- 0.398
   184 T      1.000**       4.632 +- 0.400
   316 A      0.617         3.159 +- 1.865
   318 T      0.898         4.243 +- 1.203