--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 18:30:13 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-DMB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DMB/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       -3140.05          -3168.96
2       -3140.35          -3170.82
--------------------------------------
TOTAL     -3140.19          -3170.27
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-DMB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DMB/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}           0.663532      0.002200      0.578000      0.762000      0.661000      1.001
r(A<->C){all}     0.099250      0.000298      0.067834      0.135527      0.098230      1.000
r(A<->G){all}     0.301866      0.001013      0.242159      0.366909      0.301217      1.001
r(A<->T){all}     0.091958      0.000366      0.057464      0.132579      0.090609      1.000
r(C<->G){all}     0.093428      0.000243      0.065045      0.125866      0.092812      1.000
r(C<->T){all}     0.337093      0.001033      0.275914      0.400096      0.336693      1.000
r(G<->T){all}     0.076404      0.000255      0.048028      0.110623      0.075338      1.002
pi(A){all}        0.215567      0.000172      0.190478      0.241477      0.215557      1.000
pi(C){all}        0.295597      0.000209      0.268115      0.324134      0.295584      1.000
pi(G){all}        0.255352      0.000193      0.228928      0.283234      0.254982      1.001
pi(T){all}        0.233483      0.000182      0.207177      0.260364      0.233363      1.000
alpha{1,2}        0.474332      0.022744      0.267538      0.841981      0.447767      1.002
alpha{3}         96.891434   3492.800132      5.183277    194.918592     95.429127      1.001
pinvar{all}       0.247043      0.006228      0.070681      0.385763      0.253400      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	-2873.984971
Model 7: beta	-2880.285359
Model 1: NearlyNeutral	-2880.18455
Model 2: PositiveSelection	-2874.010452


Model 2 vs 1	12.348195999999916

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_002109.2_HLA-DMB)

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

    71 S      0.995**       4.480
    75 V      0.798         3.789
    78 Q      0.919         4.212
   121 K      0.590         3.064

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_002109.2_HLA-DMB)

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

    71 S      0.991**       3.789 +- 1.303
    75 V      0.877         3.442 +- 1.478
    78 Q      0.941         3.657 +- 1.404
   121 K      0.729         3.057 +- 1.663


Model 8 vs 7	12.600776000000224

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_002109.2_HLA-DMB)

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

    71 S      0.995**       4.330
    75 V      0.813         3.718
    78 Q      0.924         4.089
   121 K      0.613         3.047

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_002109.2_HLA-DMB)

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

     2 I      0.516         1.181 +- 0.469
     3 T      0.583         1.294 +- 0.637
    16 T      0.651         1.422 +- 0.702
    37 P      0.627         1.381 +- 0.702
    56 P      0.634         1.395 +- 0.711
    59 N      0.577         1.274 +- 0.524
    60 K      0.727         1.548 +- 0.697
    71 S      0.996**       2.088 +- 0.867
    72 L      0.644         1.396 +- 0.622
    74 N      0.791         1.682 +- 0.779
    75 V      0.972*        2.048 +- 0.873
    76 L      0.794         1.686 +- 0.783
    78 Q      0.982*        2.067 +- 0.873
    79 H      0.577         1.274 +- 0.524
    82 Q      0.729         1.569 +- 0.751
    85 T      0.526         1.196 +- 0.478
    99 T      0.533         1.205 +- 0.583
   114 P      0.636         1.400 +- 0.713
   116 S      0.530         1.200 +- 0.577
   121 K      0.914         1.950 +- 0.886
   150 R      0.661         1.414 +- 0.589
   154 K      0.586         1.291 +- 0.537
   157 M      0.523         1.191 +- 0.476
   160 S      0.637         1.370 +- 0.551
   162 A      0.653         1.402 +- 0.588
   163 H      0.592         1.301 +- 0.544
   179 H      0.826         1.762 +- 0.826
   197 T      0.604         1.323 +- 0.564
   200 P      0.519         1.182 +- 0.566
   206 D      0.531         1.202 +- 0.476
   210 G      0.654         1.408 +- 0.613
   214 M      0.600         1.306 +- 0.497