--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Mar 15 01:46:38 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_A1/ENV_1_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_1/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_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -48664.19        -48704.11
2     -48660.41        -48702.51
--------------------------------------
TOTAL   -48661.08        -48703.60
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_1/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_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         7.870206    0.052154    7.441097    8.321572    7.870053    725.54    937.90    1.000
r(A<->C){all}   0.140204    0.000029    0.130070    0.150542    0.139982    359.83    400.53    1.000
r(A<->G){all}   0.293884    0.000122    0.272647    0.315905    0.293965    188.18    229.66    1.001
r(A<->T){all}   0.057949    0.000010    0.051737    0.063972    0.057912    515.89    534.92    1.002
r(C<->G){all}   0.075049    0.000025    0.066333    0.085532    0.074964    513.08    518.68    1.000
r(C<->T){all}   0.346683    0.000138    0.322485    0.368127    0.346471    213.59    254.69    1.000
r(G<->T){all}   0.086231    0.000019    0.078018    0.094919    0.086117    319.48    512.36    1.000
pi(A){all}      0.386740    0.000050    0.373746    0.401851    0.386734    210.01    306.33    1.000
pi(C){all}      0.171359    0.000025    0.161050    0.180935    0.171201    222.58    276.30    1.000
pi(G){all}      0.223939    0.000032    0.213688    0.236077    0.223881    286.80    398.06    1.000
pi(T){all}      0.217963    0.000034    0.206475    0.228823    0.218059    250.17    295.42    1.002
alpha{1,2}      0.526158    0.000651    0.476424    0.576596    0.525885    761.31    828.68    1.000
alpha{3}        1.140026    0.005302    1.004860    1.285954    1.137690   1501.00   1501.00    1.000
pinvar{all}     0.195264    0.000192    0.167768    0.220886    0.195251    672.47    836.32    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	-41627.237145
Model 2: PositiveSelection	-40951.781415
Model 0: one-ratio	-44297.988777
Model 3: discrete	-40933.806577
Model 7: beta	-41448.205743
Model 8: beta&w>1	-40858.949282


Model 0 vs 1	5341.503263999999

Model 2 vs 1	1350.911460000003

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.ZA.08.499_F5a.JQ777160_)

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

    10 C      1.000**       3.419
    12 Q      0.944         3.284
    13 W      0.591         2.430
    18 I      0.741         2.792
    27 G      0.977*        3.364
    79 H      1.000**       3.419
   125 T      0.890         3.153
   126 D      1.000**       3.419
   127 N      1.000**       3.419
   128 T      1.000**       3.419
   137 A      1.000**       3.419
   140 E      0.530         2.282
   145 K      0.999**       3.417
   148 T      0.994**       3.404
   160 S      0.999**       3.417
   161 N      1.000**       3.419
   162 S      1.000**       3.419
   163 E      0.978*        3.366
   173 T      1.000**       3.419
   182 T      0.961*        3.325
   205 T      0.534         2.291
   213 N      0.558         2.351
   249 L      0.783         2.895
   255 T      0.942         3.280
   263 S      0.958*        3.318
   265 P      1.000**       3.419
   272 N      1.000**       3.419
   280 R      0.995**       3.408
   287 F      0.865         3.094
   289 D      1.000**       3.419
   304 S      1.000**       3.419
   305 A      1.000**       3.419
   308 K      1.000**       3.419
   311 E      1.000**       3.419
   312 R      1.000**       3.419
   314 K      1.000**       3.419
   315 K      1.000**       3.419
   318 G      0.586         2.419
   320 Y      0.650         2.573
   326 D      1.000**       3.419
   328 Q      0.987*        3.387
   329 P      1.000**       3.419
   330 A      0.956*        3.313
   355 K      1.000**       3.419
   361 N      0.997**       3.413
   362 T      1.000**       3.419
   363 E      1.000**       3.419
   364 N      1.000**       3.419
   365 N      1.000**       3.419
   366 S      1.000**       3.419
   367 T      0.849         3.053
   394 A      1.000**       3.419
   396 N      1.000**       3.419
   400 V      1.000**       3.418
   414 V      1.000**       3.419
   415 N      1.000**       3.419
   416 N      1.000**       3.419
   417 N      1.000**       3.419
   418 T      1.000**       3.419
   453 E      0.996**       3.411
   467 I      0.943         3.282
   517 M      0.615         2.489
   564 S      1.000**       3.419
   570 S      0.629         2.523
   571 I      1.000**       3.419
   572 D      1.000**       3.419
   573 E      1.000**       3.419
   591 H      1.000**       3.419
   592 T      1.000**       3.419
   595 R      1.000**       3.419
   625 N      1.000**       3.419
   628 K      0.952*        3.304
   671 L      0.954*        3.309
   672 T      1.000**       3.419
   674 N      1.000**       3.419
   675 P      0.996**       3.411
   697 I      1.000**       3.419
   701 S      1.000**       3.418
   730 T      0.608         2.470
   743 T      1.000**       3.419
   747 L      0.787         2.904
   752 Q      0.989*        3.393
   784 V      0.924         3.236
   787 I      1.000**       3.419
   788 F      1.000**       3.419
   792 C      1.000**       3.419
   802 F      0.993**       3.403

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.ZA.08.499_F5a.JQ777160_)

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

    10 C      1.000**       3.500 +- 0.002
    12 Q      0.944         3.360 +- 0.575
    13 W      0.597         2.494 +- 1.226
    18 I      0.734         2.836 +- 1.104
    27 G      0.976*        3.440 +- 0.382
    79 H      1.000**       3.500 +- 0.000
   125 T      0.885         3.213 +- 0.797
   126 D      1.000**       3.500 +- 0.024
   127 N      1.000**       3.500 +- 0.000
   128 T      1.000**       3.500 +- 0.000
   137 A      1.000**       3.500 +- 0.009
   140 E      0.506         2.265 +- 1.250
   145 K      0.999**       3.498 +- 0.069
   148 T      0.994**       3.485 +- 0.195
   160 S      0.999**       3.498 +- 0.072
   161 N      1.000**       3.500 +- 0.000
   162 S      1.000**       3.500 +- 0.002
   163 E      0.977*        3.444 +- 0.371
   173 T      1.000**       3.500 +- 0.002
   182 T      0.964*        3.410 +- 0.467
   205 T      0.511         2.278 +- 1.250
   213 N      0.540         2.350 +- 1.246
   249 L      0.786         2.966 +- 1.024
   255 T      0.941         3.354 +- 0.587
   263 S      0.959*        3.398 +- 0.495
   265 P      1.000**       3.500 +- 0.002
   272 N      1.000**       3.500 +- 0.027
   280 R      0.995**       3.489 +- 0.169
   287 F      0.862         3.154 +- 0.863
   289 D      1.000**       3.500 +- 0.001
   304 S      1.000**       3.500 +- 0.000
   305 A      1.000**       3.500 +- 0.001
   308 K      1.000**       3.499 +- 0.040
   311 E      1.000**       3.500 +- 0.001
   312 R      1.000**       3.500 +- 0.000
   314 K      1.000**       3.500 +- 0.020
   315 K      1.000**       3.500 +- 0.001
   318 G      0.561         2.403 +- 1.241
   320 Y      0.644         2.609 +- 1.197
   326 D      1.000**       3.500 +- 0.000
   328 Q      0.986*        3.465 +- 0.296
   329 P      1.000**       3.500 +- 0.017
   330 A      0.959*        3.398 +- 0.493
   355 K      1.000**       3.500 +- 0.000
   361 N      0.998**       3.494 +- 0.124
   362 T      1.000**       3.500 +- 0.000
   363 E      1.000**       3.500 +- 0.000
   364 N      1.000**       3.500 +- 0.006
   365 N      1.000**       3.499 +- 0.040
   366 S      1.000**       3.500 +- 0.000
   367 T      0.844         3.110 +- 0.907
   394 A      1.000**       3.500 +- 0.001
   396 N      1.000**       3.500 +- 0.000
   400 V      1.000**       3.499 +- 0.052
   414 V      1.000**       3.500 +- 0.000
   415 N      1.000**       3.500 +- 0.000
   416 N      1.000**       3.500 +- 0.000
   417 N      1.000**       3.500 +- 0.000
   418 T      1.000**       3.500 +- 0.025
   453 E      0.996**       3.491 +- 0.149
   467 I      0.942         3.356 +- 0.583
   517 M      0.625         2.562 +- 1.211
   564 S      1.000**       3.500 +- 0.023
   570 S      0.624         2.561 +- 1.211
   571 I      1.000**       3.500 +- 0.000
   572 D      1.000**       3.500 +- 0.003
   573 E      1.000**       3.500 +- 0.006
   591 H      1.000**       3.500 +- 0.000
   592 T      1.000**       3.500 +- 0.009
   595 R      1.000**       3.500 +- 0.000
   625 N      1.000**       3.500 +- 0.009
   628 K      0.950*        3.376 +- 0.544
   671 L      0.956*        3.389 +- 0.514
   672 T      1.000**       3.500 +- 0.000
   674 N      1.000**       3.500 +- 0.001
   675 P      0.997**       3.492 +- 0.141
   697 I      1.000**       3.500 +- 0.003
   701 S      1.000**       3.499 +- 0.049
   730 T      0.595         2.488 +- 1.227
   743 T      1.000**       3.500 +- 0.000
   747 L      0.797         2.992 +- 1.006
   752 Q      0.990**       3.475 +- 0.247
   784 V      0.922         3.306 +- 0.669
   787 I      1.000**       3.500 +- 0.001
   788 F      1.000**       3.500 +- 0.000
   792 C      1.000**       3.500 +- 0.004
   802 F      0.994**       3.484 +- 0.199


Model 8 vs 7	1178.5129219999944

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.ZA.08.499_F5a.JQ777160_)

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

    10 C      1.000**       2.969
    12 Q      0.939         2.845
    13 W      0.630         2.215
    18 I      0.748         2.459
    27 G      0.969*        2.907
    79 H      1.000**       2.969
   125 T      0.884         2.734
   126 D      1.000**       2.968
   127 N      1.000**       2.969
   128 T      1.000**       2.969
   137 A      1.000**       2.969
   140 E      0.515         1.993
   145 K      0.999**       2.967
   148 T      0.992**       2.953
   160 S      0.998**       2.966
   161 N      1.000**       2.969
   162 S      1.000**       2.969
   163 E      0.972*        2.913
   173 T      1.000**       2.969
   182 T      0.966*        2.899
   205 T      0.537         2.034
   213 N      0.550         2.063
   249 L      0.795         2.552
   255 T      0.944         2.855
   263 S      0.959*        2.887
   265 P      1.000**       2.969
   272 N      1.000**       2.968
   280 R      0.993**       2.955
   287 F      0.864         2.694
   289 D      1.000**       2.969
   304 S      1.000**       2.969
   305 A      1.000**       2.969
   308 K      0.999**       2.968
   311 E      1.000**       2.969
   312 R      1.000**       2.969
   314 K      1.000**       2.968
   315 K      1.000**       2.969
   318 G      0.566         2.096
   320 Y      0.657         2.274
   326 D      1.000**       2.969
   328 Q      0.979*        2.927
   329 P      1.000**       2.969
   330 A      0.962*        2.892
   355 K      1.000**       2.969
   361 N      0.997**       2.962
   362 T      1.000**       2.969
   363 E      1.000**       2.969
   364 N      1.000**       2.969
   365 N      0.999**       2.968
   366 S      1.000**       2.969
   367 T      0.845         2.656
   394 A      1.000**       2.969
   396 N      1.000**       2.969
   400 V      0.999**       2.967
   414 V      1.000**       2.969
   415 N      1.000**       2.969
   416 N      1.000**       2.969
   417 N      1.000**       2.969
   418 T      1.000**       2.968
   453 E      0.995**       2.959
   467 I      0.935         2.839
   517 M      0.656         2.268
   564 S      1.000**       2.968
   570 S      0.678         2.316
   571 I      1.000**       2.969
   572 D      1.000**       2.969
   573 E      1.000**       2.969
   587 S      0.506         1.973
   591 H      1.000**       2.969
   592 T      1.000**       2.969
   595 R      1.000**       2.969
   625 N      1.000**       2.969
   628 K      0.941         2.851
   671 L      0.957*        2.882
   672 T      1.000**       2.969
   674 N      1.000**       2.969
   675 P      0.996**       2.961
   697 I      1.000**       2.969
   701 S      0.999**       2.967
   707 F      0.502         1.956
   730 T      0.669         2.300
   743 T      1.000**       2.969
   747 L      0.797         2.554
   752 Q      0.987*        2.942
   784 V      0.919         2.806
   787 I      1.000**       2.969
   788 F      1.000**       2.969
   792 C      1.000**       2.969
   802 F      0.990**       2.949

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.ZA.08.499_F5a.JQ777160_)

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

     7 K      0.691         2.009 +- 0.734
    10 C      1.000**       2.500 +- 0.015
    12 Q      0.987*        2.480 +- 0.179
    13 W      0.887         2.320 +- 0.505
    18 I      0.950*        2.422 +- 0.343
    27 G      0.996**       2.494 +- 0.103
    59 V      0.587         1.848 +- 0.778
    79 H      1.000**       2.500 +- 0.015
   125 T      0.982*        2.472 +- 0.210
   126 D      1.000**       2.500 +- 0.018
   127 N      1.000**       2.500 +- 0.015
   128 T      1.000**       2.500 +- 0.015
   137 A      1.000**       2.500 +- 0.016
   140 E      0.921         2.377 +- 0.422
   145 K      0.999**       2.499 +- 0.041
   148 T      0.998**       2.497 +- 0.070
   160 S      1.000**       2.500 +- 0.029
   161 N      1.000**       2.500 +- 0.015
   162 S      1.000**       2.500 +- 0.015
   163 E      0.995**       2.493 +- 0.108
   173 T      1.000**       2.500 +- 0.015
   182 T      0.988*        2.482 +- 0.169
   205 T      0.921         2.376 +- 0.424
   211 P      0.569         1.818 +- 0.785
   213 N      0.924         2.380 +- 0.417
   249 L      0.947         2.416 +- 0.356
   255 T      0.989*        2.483 +- 0.163
   263 S      0.990**       2.485 +- 0.156
   265 P      1.000**       2.500 +- 0.015
   272 N      1.000**       2.500 +- 0.021
   280 R      0.998**       2.498 +- 0.064
   287 F      0.975*        2.461 +- 0.245
   289 D      1.000**       2.500 +- 0.015
   303 R      0.649         1.949 +- 0.750
   304 S      1.000**       2.500 +- 0.015
   305 A      1.000**       2.500 +- 0.015
   308 K      1.000**       2.500 +- 0.023
   311 E      1.000**       2.500 +- 0.015
   312 R      1.000**       2.500 +- 0.015
   314 K      1.000**       2.500 +- 0.019
   315 K      1.000**       2.500 +- 0.015
   318 G      0.937         2.402 +- 0.380
   320 Y      0.926         2.383 +- 0.415
   326 D      1.000**       2.500 +- 0.015
   328 Q      0.997**       2.496 +- 0.083
   329 P      1.000**       2.500 +- 0.018
   330 A      0.987*        2.479 +- 0.181
   355 K      1.000**       2.500 +- 0.015
   361 N      0.999**       2.498 +- 0.061
   362 T      1.000**       2.500 +- 0.015
   363 E      1.000**       2.500 +- 0.015
   364 N      1.000**       2.500 +- 0.016
   365 N      1.000**       2.500 +- 0.023
   366 S      1.000**       2.500 +- 0.015
   367 T      0.973*        2.458 +- 0.254
   394 A      1.000**       2.500 +- 0.015
   396 N      1.000**       2.500 +- 0.015
   400 V      1.000**       2.500 +- 0.027
   414 V      1.000**       2.500 +- 0.015
   415 N      1.000**       2.500 +- 0.015
   416 N      1.000**       2.500 +- 0.015
   417 N      1.000**       2.500 +- 0.015
   418 T      1.000**       2.500 +- 0.022
   453 E      0.999**       2.499 +- 0.054
   467 I      0.989*        2.483 +- 0.165
   487 I      0.731         2.077 +- 0.697
   517 M      0.891         2.327 +- 0.496
   559 N      0.835         2.241 +- 0.585
   564 S      1.000**       2.500 +- 0.020
   570 S      0.926         2.384 +- 0.413
   571 I      1.000**       2.500 +- 0.015
   572 D      1.000**       2.500 +- 0.015
   573 E      1.000**       2.500 +- 0.016
   587 S      0.925         2.382 +- 0.414
   591 H      1.000**       2.500 +- 0.015
   592 T      1.000**       2.500 +- 0.016
   595 R      1.000**       2.500 +- 0.015
   625 N      1.000**       2.500 +- 0.016
   628 K      0.992**       2.487 +- 0.143
   671 L      0.989*        2.482 +- 0.167
   672 T      1.000**       2.500 +- 0.015
   674 N      1.000**       2.500 +- 0.015
   675 P      0.998**       2.498 +- 0.067
   697 I      1.000**       2.500 +- 0.016
   701 S      1.000**       2.500 +- 0.026
   707 F      0.870         2.295 +- 0.532
   709 D      0.634         1.921 +- 0.764
   721 R      0.618         1.885 +- 0.784
   730 T      0.936         2.399 +- 0.387
   743 T      1.000**       2.500 +- 0.015
   747 L      0.932         2.392 +- 0.401
   752 Q      0.995**       2.492 +- 0.114
   766 L      0.645         1.936 +- 0.762
   783 I      0.755         2.114 +- 0.677
   784 V      0.986*        2.479 +- 0.182
   787 I      1.000**       2.500 +- 0.015
   788 F      1.000**       2.500 +- 0.015
   792 C      1.000**       2.500 +- 0.016
   802 F      0.997**       2.496 +- 0.087