--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Feb 10 23:10:08 WET 2018
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/HIV1_N2/POL_1_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)

(Values are saved to the file /opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -30003.54        -30045.47
2     -30005.35        -30046.08
--------------------------------------
TOTAL   -30004.08        -30045.82
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         3.120844    0.007473    2.950945    3.289556    3.118392   1167.33   1206.02    1.000
r(A<->C){all}   0.077608    0.000016    0.069511    0.085079    0.077500    657.56    717.87    1.000
r(A<->G){all}   0.345174    0.000152    0.321095    0.368907    0.345328    309.57    401.82    1.002
r(A<->T){all}   0.033282    0.000005    0.028743    0.037685    0.033200    593.55    786.45    1.000
r(C<->G){all}   0.040371    0.000017    0.032272    0.048584    0.040184    698.10    732.12    1.001
r(C<->T){all}   0.462310    0.000178    0.436367    0.488444    0.462479    363.85    441.23    1.001
r(G<->T){all}   0.041256    0.000013    0.035061    0.048820    0.041127    730.29    803.33    1.000
pi(A){all}      0.410060    0.000050    0.395844    0.422988    0.410183    791.09    867.55    1.000
pi(C){all}      0.169847    0.000030    0.158516    0.180136    0.169835    603.97    626.13    1.002
pi(G){all}      0.203739    0.000029    0.193303    0.214697    0.203627    608.08    715.16    1.000
pi(T){all}      0.216353    0.000036    0.204959    0.228330    0.216299    762.62    798.84    1.000
alpha{1,2}      0.289572    0.000206    0.263101    0.318406    0.288809    889.74    994.56    1.000
alpha{3}        2.404885    0.060077    1.939702    2.864435    2.387794   1179.84   1245.41    1.000
pinvar{all}     0.266603    0.000297    0.233151    0.299325    0.266780    940.60   1053.83    1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.


Setting sumt conformat to Simple



 --- CODEML SUMMARY

Model 1: NearlyNeutral	-29370.480694
Model 2: PositiveSelection	-29291.241634
Model 0: one-ratio	-30818.626155
Model 3: discrete	-29164.468606
Model 7: beta	-29225.191414
Model 8: beta&w>1	-29118.940595


Model 0 vs 1	2896.290922

Model 2 vs 1	158.47811999999976

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.US.00.ES1_20.EF363123_)

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

    17 S      0.919         2.792
    33 S      0.993**       2.937
    34 L      1.000**       2.951
    41 T      0.953*        2.859
    42 L      0.985*        2.923
    43 S      0.960*        2.874
    54 L      0.851         2.661
   107 P      1.000**       2.951
   266 E      1.000**       2.951
   278 T      0.719         2.403
   305 S      0.865         2.688
   350 Q      0.591         2.153
   354 K      0.988*        2.927
   388 V      0.767         2.497
   429 T      0.614         2.198
   519 T      0.542         2.057
   611 S      0.947         2.847
   626 H      1.000**       2.951
   697 A      1.000**       2.951
   775 I      0.902         2.761
   804 I      0.978*        2.909

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: B.US.00.ES1_20.EF363123_)

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

    17 S      0.949         2.441 +- 0.360
    21 T      0.544         1.821 +- 0.755
    32 R      0.825         2.241 +- 0.573
    33 S      0.992**       2.507 +- 0.191
    34 L      1.000**       2.519 +- 0.137
    41 T      0.978*        2.486 +- 0.258
    42 L      0.990**       2.504 +- 0.203
    43 S      0.981*        2.490 +- 0.248
    54 L      0.908         2.379 +- 0.458
   107 P      1.000**       2.519 +- 0.137
   266 E      1.000**       2.519 +- 0.137
   278 T      0.921         2.390 +- 0.418
   305 S      0.952*        2.442 +- 0.347
   350 Q      0.825         2.246 +- 0.582
   354 K      0.993**       2.508 +- 0.186
   388 V      0.894         2.355 +- 0.482
   429 T      0.796         2.205 +- 0.619
   503 A      0.686         2.036 +- 0.706
   519 T      0.742         2.123 +- 0.670
   611 S      0.960*        2.459 +- 0.325
   626 H      1.000**       2.519 +- 0.137
   660 L      0.580         1.873 +- 0.745
   697 A      1.000**       2.519 +- 0.137
   775 I      0.952*        2.445 +- 0.351
   804 I      0.985*        2.496 +- 0.229
   826 T      0.726         2.094 +- 0.675


Model 8 vs 7	212.50163800000155

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.US.00.ES1_20.EF363123_)

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

     5 N      0.945         1.963
    12 K      0.678         1.594
    16 L      0.688         1.607
    17 S      0.996**       2.033
    21 T      0.912         1.917
    32 R      0.998**       2.036
    33 S      0.999**       2.038
    34 L      1.000**       2.039
    41 T      0.999**       2.038
    42 L      1.000**       2.038
    43 S      0.999**       2.038
    44 F      0.783         1.736
    54 L      0.988*        2.023
    81 N      0.853         1.836
   107 P      1.000**       2.039
   137 I      0.523         1.378
   266 E      1.000**       2.039
   278 T      0.999**       2.038
   305 S      0.999**       2.037
   350 Q      0.993**       2.029
   354 K      1.000**       2.038
   357 F      0.631         1.527
   388 V      0.995**       2.032
   420 R      0.906         1.910
   429 T      0.981*        2.012
   477 Q      0.886         1.881
   503 A      0.965*        1.990
   519 T      0.969*        1.995
   520 T      0.948         1.967
   578 V      0.930         1.942
   595 S      0.915         1.921
   611 S      0.996**       2.034
   626 H      1.000**       2.039
   660 L      0.952*        1.973
   674 I      0.508         1.353
   697 A      1.000**       2.039
   731 L      0.543         1.390
   775 I      0.998**       2.036
   777 L      0.755         1.695
   804 I      0.999**       2.038
   826 T      0.985*        2.018

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: B.US.00.ES1_20.EF363123_)

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

    17 S      0.985*        2.476 +- 0.196
    21 T      0.740         2.077 +- 0.717
    32 R      0.866         2.288 +- 0.538
    33 S      0.998**       2.497 +- 0.063
    34 L      1.000**       2.500 +- 0.001
    41 T      0.991**       2.486 +- 0.146
    42 L      0.997**       2.495 +- 0.088
    43 S      0.993**       2.488 +- 0.135
    44 F      0.574         1.796 +- 0.823
    54 L      0.965*        2.444 +- 0.295
   107 P      1.000**       2.500 +- 0.002
   266 E      1.000**       2.500 +- 0.001
   278 T      0.947         2.417 +- 0.351
   305 S      0.977*        2.464 +- 0.237
   350 Q      0.897         2.337 +- 0.482
   354 K      0.998**       2.496 +- 0.075
   388 V      0.953*        2.425 +- 0.337
   429 T      0.915         2.364 +- 0.448
   503 A      0.843         2.247 +- 0.587
   519 T      0.887         2.318 +- 0.512
   595 S      0.523         1.733 +- 0.807
   611 S      0.990*        2.483 +- 0.163
   626 H      1.000**       2.500 +- 0.003
   660 L      0.717         2.044 +- 0.726
   697 A      1.000**       2.500 +- 0.004
   775 I      0.983*        2.472 +- 0.208
   777 L      0.620         1.864 +- 0.818
   804 I      0.996**       2.493 +- 0.105
   826 T      0.844         2.251 +- 0.580