--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Jan 26 22:08:29 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_N1/ENV_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_5/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_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -50178.64        -50224.08
2     -50179.17        -50220.14
--------------------------------------
TOTAL   -50178.87        -50223.40
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_5/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_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        10.502673    0.113840    9.911662   11.254180   10.489470    540.52    564.12    1.000
r(A<->C){all}   0.141198    0.000028    0.130787    0.151783    0.141111    350.49    481.77    1.002
r(A<->G){all}   0.289300    0.000094    0.271531    0.309303    0.289369    222.86    264.27    1.000
r(A<->T){all}   0.060100    0.000011    0.053249    0.065929    0.060004    518.94    535.03    1.000
r(C<->G){all}   0.075266    0.000026    0.065774    0.085408    0.075119    332.14    416.09    1.000
r(C<->T){all}   0.345880    0.000115    0.326707    0.368560    0.345459    217.80    246.73    1.000
r(G<->T){all}   0.088255    0.000021    0.079731    0.097180    0.088078    566.48    611.17    1.000
pi(A){all}      0.382923    0.000039    0.370105    0.394352    0.382881    331.65    382.85    1.000
pi(C){all}      0.172784    0.000023    0.162919    0.181803    0.172567    326.70    353.17    1.000
pi(G){all}      0.223296    0.000024    0.214625    0.233386    0.223227    295.07    330.66    1.000
pi(T){all}      0.220997    0.000031    0.210570    0.231729    0.221041    303.92    340.84    1.000
alpha{1,2}      0.446200    0.000386    0.408614    0.486364    0.445813   1015.32   1069.44    1.000
alpha{3}        1.031890    0.003635    0.918539    1.150164    1.031327   1105.13   1182.38    1.000
pinvar{all}     0.095988    0.000176    0.069434    0.120952    0.095957    979.26    993.45    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	-40904.63629
Model 2: PositiveSelection	-40275.298151
Model 0: one-ratio	-43299.134088
Model 3: discrete	-40230.339606
Model 7: beta	-40738.792083
Model 8: beta&w>1	-40146.38401


Model 0 vs 1	4788.995595999993

Model 2 vs 1	1258.676277999999

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BW.96.96BW11B01.AF110971_)

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

    18 G      0.587         2.468
    51 V      0.729         2.824
    71 V      1.000**       3.503
   118 N      0.999**       3.500
   119 T      1.000**       3.503
   120 V      1.000**       3.503
   121 N      1.000**       3.503
   122 D      1.000**       3.503
   123 T      1.000**       3.503
   124 L      1.000**       3.503
   125 H      1.000**       3.503
   134 V      0.978*        3.447
   140 R      0.804         3.013
   142 Y      0.918         3.296
   148 L      0.915         3.290
   152 P      0.925         3.316
   154 N      1.000**       3.503
   155 N      1.000**       3.503
   156 K      1.000**       3.503
   157 E      1.000**       3.503
   174 S      0.995**       3.490
   203 N      1.000**       3.503
   240 I      0.718         2.797
   252 E      0.794         2.988
   255 E      0.998**       3.499
   262 N      0.872         3.182
   270 R      1.000**       3.503
   280 A      0.998**       3.498
   294 E      1.000**       3.503
   295 S      1.000**       3.503
   296 Q      1.000**       3.503
   299 N      0.980*        3.452
   302 Q      1.000**       3.503
   303 R      1.000**       3.503
   305 S      1.000**       3.503
   306 E      1.000**       3.503
   309 K      0.864         3.162
   311 H      0.929         3.324
   317 K      1.000**       3.503
   319 N      1.000**       3.502
   320 Q      1.000**       3.503
   321 P      1.000**       3.503
   345 K      1.000**       3.503
   346 Y      1.000**       3.503
   347 I      1.000**       3.503
   348 T      1.000**       3.503
   375 A      1.000**       3.503
   377 N      1.000**       3.503
   381 K      1.000**       3.503
   394 K      1.000**       3.503
   395 N      1.000**       3.503
   396 D      1.000**       3.503
   428 K      0.997**       3.496
   532 A      1.000**       3.502
   537 A      0.983*        3.460
   544 Q      1.000**       3.503
   545 E      1.000**       3.503
   546 E      0.999**       3.501
   549 G      1.000**       3.503
   565 D      1.000**       3.503
   566 T      1.000**       3.503
   569 R      1.000**       3.503
   573 V      0.989*        3.476
   599 D      1.000**       3.503
   646 T      1.000**       3.503
   648 N      0.696         2.743
   649 P      0.533         2.335
   671 I      1.000**       3.503
   672 R      0.970*        3.427
   675 S      0.645         2.614
   681 A      1.000**       3.503
   705 R      0.775         2.940
   710 I      0.999**       3.500
   719 Q      0.943         3.359
   750 L      0.529         2.324
   751 I      0.980*        3.453
   754 I      0.997**       3.496
   755 G      0.998**       3.497
   759 R      0.733         2.834
   769 F      0.995**       3.491

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: C.BW.96.96BW11B01.AF110971_)

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

    18 G      0.678         2.695 +- 1.168
    51 V      0.797         2.994 +- 1.005
    71 V      1.000**       3.500 +- 0.001
   118 N      0.999**       3.498 +- 0.071
   119 T      1.000**       3.500 +- 0.013
   120 V      1.000**       3.500 +- 0.000
   121 N      1.000**       3.500 +- 0.000
   122 D      1.000**       3.500 +- 0.001
   123 T      1.000**       3.500 +- 0.000
   124 L      1.000**       3.500 +- 0.000
   125 H      1.000**       3.500 +- 0.000
   134 V      0.984*        3.461 +- 0.309
   140 R      0.857         3.142 +- 0.876
   142 Y      0.941         3.353 +- 0.587
   148 L      0.940         3.349 +- 0.596
   152 P      0.947         3.368 +- 0.559
   154 N      1.000**       3.500 +- 0.015
   155 N      1.000**       3.500 +- 0.000
   156 K      1.000**       3.500 +- 0.000
   157 E      1.000**       3.500 +- 0.000
   174 S      0.996**       3.491 +- 0.149
   203 N      1.000**       3.500 +- 0.015
   240 I      0.788         2.971 +- 1.021
   252 E      0.849         3.123 +- 0.894
   255 E      0.999**       3.497 +- 0.085
   262 N      0.908         3.270 +- 0.723
   270 R      1.000**       3.500 +- 0.002
   280 A      0.999**       3.497 +- 0.089
   294 E      1.000**       3.500 +- 0.001
   295 S      1.000**       3.500 +- 0.000
   296 Q      1.000**       3.500 +- 0.001
   299 N      0.986*        3.464 +- 0.296
   302 Q      1.000**       3.500 +- 0.002
   303 R      1.000**       3.500 +- 0.000
   305 S      1.000**       3.500 +- 0.000
   306 E      1.000**       3.500 +- 0.000
   309 K      0.902         3.255 +- 0.743
   311 H      0.949         3.374 +- 0.548
   317 K      1.000**       3.500 +- 0.000
   319 N      1.000**       3.499 +- 0.039
   320 Q      1.000**       3.500 +- 0.000
   321 P      1.000**       3.500 +- 0.003
   345 K      1.000**       3.500 +- 0.000
   346 Y      1.000**       3.500 +- 0.001
   347 I      1.000**       3.500 +- 0.000
   348 T      1.000**       3.500 +- 0.003
   375 A      1.000**       3.500 +- 0.003
   377 N      1.000**       3.500 +- 0.000
   381 K      1.000**       3.500 +- 0.006
   394 K      1.000**       3.500 +- 0.000
   395 N      1.000**       3.500 +- 0.000
   396 D      1.000**       3.500 +- 0.000
   428 K      0.998**       3.495 +- 0.106
   532 A      1.000**       3.500 +- 0.024
   537 A      0.988*        3.470 +- 0.271
   544 Q      1.000**       3.500 +- 0.000
   545 E      1.000**       3.500 +- 0.004
   546 E      1.000**       3.499 +- 0.051
   549 G      1.000**       3.500 +- 0.004
   565 D      1.000**       3.500 +- 0.000
   566 T      1.000**       3.500 +- 0.015
   569 R      1.000**       3.500 +- 0.000
   573 V      0.993**       3.481 +- 0.216
   599 D      1.000**       3.500 +- 0.004
   646 T      1.000**       3.500 +- 0.013
   648 N      0.771         2.927 +- 1.051
   649 P      0.629         2.572 +- 1.208
   671 I      1.000**       3.500 +- 0.003
   672 R      0.979*        3.446 +- 0.362
   675 S      0.728         2.820 +- 1.112
   681 A      1.000**       3.500 +- 0.004
   705 R      0.834         3.085 +- 0.930
   710 I      0.999**       3.498 +- 0.072
   719 Q      0.959*        3.398 +- 0.494
   750 L      0.625         2.563 +- 1.210
   751 I      0.986*        3.465 +- 0.293
   754 I      0.998**       3.495 +- 0.110
   755 G      0.998**       3.496 +- 0.099
   759 R      0.800         3.001 +- 0.999
   769 F      0.997**       3.492 +- 0.142


Model 8 vs 7	1184.8161459999974

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BW.96.96BW11B01.AF110971_)

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

    18 G      0.819         2.598
    51 V      0.879         2.721
    71 V      1.000**       2.973
   118 N      0.999**       2.971
   119 T      1.000**       2.972
   120 V      1.000**       2.973
   121 N      1.000**       2.973
   122 D      1.000**       2.973
   123 T      1.000**       2.973
   124 L      1.000**       2.973
   125 H      1.000**       2.973
   134 V      0.991**       2.954
   140 R      0.913         2.792
   142 Y      0.965*        2.901
   148 L      0.960*        2.891
   152 P      0.969*        2.909
   154 N      1.000**       2.972
   155 N      1.000**       2.973
   156 K      1.000**       2.973
   157 E      1.000**       2.973
   174 S      0.998**       2.968
   203 N      1.000**       2.972
   240 I      0.853         2.665
   252 E      0.918         2.803
   253 S      0.608         2.152
   255 E      0.999**       2.971
   262 N      0.940         2.848
   270 R      1.000**       2.973
   280 A      0.999**       2.971
   294 E      1.000**       2.973
   295 S      1.000**       2.973
   296 Q      1.000**       2.973
   299 N      0.991**       2.954
   302 Q      1.000**       2.973
   303 R      1.000**       2.973
   305 S      1.000**       2.973
   306 E      1.000**       2.973
   309 K      0.943         2.854
   311 H      0.965*        2.901
   317 K      1.000**       2.973
   319 N      1.000**       2.972
   320 Q      1.000**       2.973
   321 P      1.000**       2.973
   345 K      1.000**       2.973
   346 Y      1.000**       2.973
   347 I      1.000**       2.973
   348 T      1.000**       2.973
   375 A      1.000**       2.973
   377 N      1.000**       2.973
   381 K      1.000**       2.972
   394 K      1.000**       2.973
   395 N      1.000**       2.973
   396 D      1.000**       2.973
   428 K      0.999**       2.970
   532 A      1.000**       2.972
   537 A      0.992**       2.956
   544 Q      1.000**       2.973
   545 E      1.000**       2.973
   546 E      1.000**       2.972
   549 G      1.000**       2.973
   565 D      1.000**       2.973
   566 T      1.000**       2.972
   569 R      1.000**       2.973
   573 V      0.996**       2.963
   599 D      1.000**       2.973
   602 K      0.509         1.956
   646 T      1.000**       2.972
   648 N      0.856         2.673
   649 P      0.733         2.413
   671 I      1.000**       2.973
   672 R      0.971*        2.913
   675 S      0.829         2.620
   681 A      1.000**       2.973
   705 R      0.885         2.733
   710 I      0.999**       2.971
   719 Q      0.966*        2.902
   750 L      0.754         2.464
   751 I      0.992**       2.955
   754 I      0.999**       2.970
   755 G      0.999**       2.970
   759 R      0.864         2.689
   769 F      0.996**       2.965

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: C.BW.96.96BW11B01.AF110971_)

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

    18 G      0.753         2.224 +- 0.805
    48 E      0.542         1.790 +- 0.812
    51 V      0.827         2.411 +- 0.778
    71 V      1.000**       2.836 +- 0.472
   118 N      0.999**       2.832 +- 0.477
   119 T      1.000**       2.836 +- 0.472
   120 V      1.000**       2.836 +- 0.472
   121 N      1.000**       2.836 +- 0.472
   122 D      1.000**       2.836 +- 0.472
   123 T      1.000**       2.836 +- 0.472
   124 L      1.000**       2.836 +- 0.472
   125 H      1.000**       2.836 +- 0.472
   134 V      0.971*        2.762 +- 0.558
   140 R      0.866         2.507 +- 0.741
   142 Y      0.953*        2.723 +- 0.605
   148 L      0.940         2.691 +- 0.630
   152 P      0.946         2.703 +- 0.617
   154 N      1.000**       2.836 +- 0.472
   155 N      1.000**       2.836 +- 0.472
   156 K      1.000**       2.836 +- 0.472
   157 E      1.000**       2.836 +- 0.472
   174 S      0.997**       2.830 +- 0.482
   203 N      1.000**       2.836 +- 0.472
   240 I      0.847         2.478 +- 0.782
   244 A      0.533         1.786 +- 0.851
   252 E      0.853         2.469 +- 0.750
   253 S      0.664         2.061 +- 0.881
   255 E      0.998**       2.832 +- 0.477
   262 N      0.908         2.610 +- 0.688
   270 R      1.000**       2.836 +- 0.472
   280 A      0.999**       2.833 +- 0.477
   287 E      0.605         1.913 +- 0.832
   294 E      1.000**       2.836 +- 0.472
   295 S      1.000**       2.836 +- 0.472
   296 Q      1.000**       2.836 +- 0.472
   299 N      0.982*        2.791 +- 0.529
   302 Q      1.000**       2.836 +- 0.472
   303 R      1.000**       2.836 +- 0.472
   305 S      1.000**       2.836 +- 0.472
   306 E      1.000**       2.836 +- 0.472
   309 K      0.896         2.579 +- 0.701
   311 H      0.952*        2.720 +- 0.607
   317 K      1.000**       2.836 +- 0.472
   319 N      1.000**       2.835 +- 0.473
   320 Q      1.000**       2.836 +- 0.472
   321 P      1.000**       2.836 +- 0.472
   345 K      1.000**       2.836 +- 0.472
   346 Y      1.000**       2.836 +- 0.472
   347 I      1.000**       2.836 +- 0.472
   348 T      1.000**       2.836 +- 0.472
   375 A      1.000**       2.836 +- 0.472
   377 N      1.000**       2.836 +- 0.472
   381 K      1.000**       2.836 +- 0.472
   394 K      1.000**       2.836 +- 0.472
   395 N      1.000**       2.836 +- 0.472
   396 D      1.000**       2.836 +- 0.472
   428 K      0.998**       2.831 +- 0.480
   532 A      1.000**       2.836 +- 0.473
   537 A      0.990*        2.812 +- 0.506
   544 Q      1.000**       2.836 +- 0.472
   545 E      1.000**       2.836 +- 0.472
   546 E      0.999**       2.835 +- 0.474
   549 G      1.000**       2.836 +- 0.472
   561 S      0.505         1.725 +- 0.809
   565 D      1.000**       2.836 +- 0.472
   566 T      1.000**       2.836 +- 0.472
   569 R      1.000**       2.836 +- 0.472
   573 V      0.989*        2.809 +- 0.507
   599 D      1.000**       2.836 +- 0.472
   602 K      0.617         1.932 +- 0.820
   646 T      1.000**       2.836 +- 0.472
   648 N      0.829         2.425 +- 0.788
   649 P      0.757         2.276 +- 0.863
   671 I      1.000**       2.836 +- 0.472
   672 R      0.974*        2.781 +- 0.559
   675 S      0.772         2.275 +- 0.806
   681 A      1.000**       2.836 +- 0.472
   695 R      0.556         1.842 +- 0.886
   705 R      0.881         2.560 +- 0.742
   710 I      0.999**       2.834 +- 0.475
   719 Q      0.962*        2.748 +- 0.586
   733 L      0.536         1.793 +- 0.868
   750 L      0.737         2.199 +- 0.825
   751 I      0.984*        2.797 +- 0.522
   754 I      0.998**       2.831 +- 0.479
   755 G      0.999**       2.833 +- 0.477
   759 R      0.857         2.499 +- 0.770
   769 F      0.996**       2.827 +- 0.486