--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Apr 11 16:41:35 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-C/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-C/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       -2201.93          -2212.00
2       -2201.72          -2211.50
--------------------------------------
TOTAL     -2201.82          -2211.78
--------------------------------------


Model parameter summaries over the runs sampled in files
"/home/jorge/Data/ADOPS/HLA/HLA-C/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-C/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}           0.153378      0.000348      0.121000      0.194000      0.152000      1.000
r(A<->C){all}     0.174749      0.001467      0.107554      0.255721      0.172343      1.000
r(A<->G){all}     0.324630      0.002602      0.230865      0.431846      0.322444      1.001
r(A<->T){all}     0.093258      0.001647      0.026583      0.182979      0.089277      1.000
r(C<->G){all}     0.066932      0.000408      0.032570      0.111913      0.065296      1.001
r(C<->T){all}     0.248857      0.002409      0.160052      0.351556      0.245570      1.000
r(G<->T){all}     0.091573      0.000899      0.041045      0.157659      0.088704      1.000
pi(A){all}        0.198705      0.000134      0.176542      0.221935      0.198423      1.000
pi(C){all}        0.308291      0.000181      0.282091      0.334931      0.308300      1.000
pi(G){all}        0.336199      0.000192      0.309184      0.363398      0.336024      1.000
pi(T){all}        0.156804      0.000112      0.136500      0.178466      0.156590      1.000
alpha{1,2}       82.406501   4003.004596      0.372055    193.337012     77.504659      1.002
alpha{3}        103.533438   3171.092922      9.735424    195.283904    103.721452      1.001
pinvar{all}       0.777500      0.003801      0.615880      0.847185      0.790397      1.002
---------------------------------------------------------------------------------------------
* 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	-2152.118753
Model 7: beta	-2165.809291
Model 1: NearlyNeutral	-2165.808156
Model 2: PositiveSelection	-2152.140463


Model 2 vs 1	27.335385999999744

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_002108.4_HLA-C)

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

    48 S      0.866         10.052
    97 A      0.983*        11.280
   104 N      0.548         6.705
   121 R      0.995**       11.403
   138 D      0.938         10.809
   140 S      0.860         9.993
   171 L      0.574         6.984
   180 L      0.989*        11.342
   187 T      0.991**       11.360
   329 A      0.813         9.495
   362 T      0.814         9.500

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_002108.4_HLA-C)

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

    48 S      0.866         7.729 +- 3.045
    97 A      0.980*        8.636 +- 1.860
   104 N      0.622         5.727 +- 4.002
   121 R      0.994**       8.743 +- 1.630
   138 D      0.958*        8.451 +- 2.159
   140 S      0.899         7.980 +- 2.759
   171 L      0.671         6.115 +- 3.892
   180 L      0.987*        8.692 +- 1.744
   187 T      0.991**       8.719 +- 1.683
   329 A      0.828         7.418 +- 3.289
   362 T      0.829         7.426 +- 3.283


Model 8 vs 7	27.381075999999666

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_002108.4_HLA-C)

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

    48 S      0.874         10.006
    97 A      0.986*        11.184
   104 N      0.558         6.679
   121 R      0.996**       11.290
   138 D      0.954*        10.844
   140 S      0.882         10.092
   171 L      0.590         7.019
   180 L      0.991**       11.236
   187 T      0.993**       11.259
   329 A      0.823         9.473
   362 T      0.824         9.479

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_002108.4_HLA-C)

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

    48 S      0.898         8.060 +- 2.808
    97 A      0.989*        8.782 +- 1.631
   104 N      0.669         6.157 +- 4.030
   121 R      0.997**       8.849 +- 1.456
   138 D      0.980*        8.706 +- 1.789
   140 S      0.938         8.366 +- 2.382
   171 L      0.723         6.590 +- 3.851
   180 L      0.993**       8.815 +- 1.548
   187 T      0.996**       8.838 +- 1.485
   208 P      0.542         5.065 +- 4.181
   329 A      0.867         7.800 +- 3.074
   362 T      0.868         7.807 +- 3.066