--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Mar 18 03:59:30 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_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -48140.15        -48190.84
2     -48143.73        -48181.76
--------------------------------------
TOTAL   -48140.82        -48190.14
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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}         7.924580    0.038989    7.531423    8.295759    7.921610    997.89   1115.63    1.000
r(A<->C){all}   0.137237    0.000026    0.127058    0.146250    0.137221    494.31    571.21    1.003
r(A<->G){all}   0.291069    0.000096    0.272852    0.310744    0.290791    208.45    262.94    1.008
r(A<->T){all}   0.058761    0.000009    0.052875    0.064499    0.058707    487.19    582.07    1.000
r(C<->G){all}   0.075342    0.000023    0.066137    0.084448    0.075257    465.61    488.87    1.000
r(C<->T){all}   0.346549    0.000111    0.325588    0.365750    0.346818    205.62    250.05    1.014
r(G<->T){all}   0.091042    0.000019    0.082465    0.099355    0.091067    640.52    641.94    1.000
pi(A){all}      0.389313    0.000041    0.377038    0.402714    0.389421    186.84    288.88    1.007
pi(C){all}      0.175724    0.000022    0.166923    0.185081    0.175724    295.69    404.61    1.002
pi(G){all}      0.216852    0.000026    0.206623    0.226496    0.216820    364.09    377.65    1.002
pi(T){all}      0.218110    0.000031    0.207745    0.229529    0.218010    462.31    482.06    1.009
alpha{1,2}      0.447391    0.000379    0.408282    0.483509    0.446617   1170.88   1257.11    1.000
alpha{3}        1.030798    0.004949    0.902775    1.171946    1.028718   1217.04   1259.96    1.000
pinvar{all}     0.143854    0.000182    0.116537    0.168512    0.144010    949.51   1031.44    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	-39389.370011
Model 2: PositiveSelection	-38756.699399
Model 0: one-ratio	-41701.418989
Model 3: discrete	-38738.678452
Model 7: beta	-39270.501835
Model 8: beta&w>1	-38676.877865


Model 0 vs 1	4624.097955999998

Model 2 vs 1	1265.3412240000034

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.GB.08.D650_E9.HQ595775_)

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

     7 R      1.000**       3.625
    10 H      0.993**       3.609
    14 T      0.525         2.377
    77 E      1.000**       3.626
   126 N      1.000**       3.626
   127 S      1.000**       3.626
   128 S      1.000**       3.626
   129 E      1.000**       3.626
   130 E      1.000**       3.626
   131 R      1.000**       3.626
   132 G      1.000**       3.626
   149 Q      0.999**       3.624
   152 Y      0.911         3.393
   164 D      1.000**       3.626
   165 N      1.000**       3.626
   166 T      1.000**       3.625
   167 T      1.000**       3.626
   177 V      0.822         3.160
   184 S      0.999**       3.625
   215 T      0.973*        3.554
   252 L      0.987*        3.593
   254 D      0.834         3.189
   256 T      0.945         3.481
   268 E      1.000**       3.626
   275 N      1.000**       3.626
   283 H      1.000**       3.626
   294 E      1.000**       3.626
   302 E      1.000**       3.626
   305 Y      1.000**       3.626
   306 Q      1.000**       3.626
   308 V      1.000**       3.626
   309 E      1.000**       3.626
   314 Q      0.996**       3.616
   319 V      1.000**       3.626
   321 D      1.000**       3.626
   322 Q      0.997**       3.618
   323 S      1.000**       3.626
   348 Q      1.000**       3.626
   378 S      1.000**       3.626
   380 P      1.000**       3.626
   384 T      1.000**       3.626
   398 N      1.000**       3.626
   399 N      1.000**       3.626
   400 D      1.000**       3.626
   401 T      1.000**       3.626
   436 R      1.000**       3.626
   542 A      0.998**       3.620
   547 N      1.000**       3.626
   554 L      1.000**       3.626
   555 E      1.000**       3.626
   556 Y      1.000**       3.626
   564 Q      0.984*        3.584
   570 D      0.980*        3.573
   574 N      1.000**       3.626
   575 L      0.984*        3.583
   578 T      1.000**       3.626
   608 D      0.998**       3.620
   654 H      0.514         2.349
   655 H      1.000**       3.626
   657 A      0.976*        3.564
   658 P      0.700         2.839
   680 G      0.999**       3.625
   720 A      0.998**       3.620
   760 I      0.995**       3.614
   761 V      0.989*        3.596
   764 T      1.000**       3.626
   765 Y      1.000**       3.626
   769 L      0.998**       3.621
   779 L      0.840         3.206

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.GB.08.D650_E9.HQ595775_)

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

     7 R      1.000**       3.499 +- 0.054
    10 H      0.994**       3.484 +- 0.198
    14 T      0.564         2.409 +- 1.240
    77 E      1.000**       3.500 +- 0.000
   125 D      0.507         2.268 +- 1.250
   126 N      1.000**       3.500 +- 0.000
   127 S      1.000**       3.500 +- 0.000
   128 S      1.000**       3.500 +- 0.000
   129 E      1.000**       3.500 +- 0.000
   130 E      1.000**       3.500 +- 0.000
   131 R      1.000**       3.500 +- 0.000
   132 G      1.000**       3.500 +- 0.000
   149 Q      0.999**       3.498 +- 0.062
   152 Y      0.920         3.301 +- 0.677
   164 D      1.000**       3.500 +- 0.000
   165 N      1.000**       3.500 +- 0.000
   166 T      1.000**       3.499 +- 0.037
   167 T      1.000**       3.500 +- 0.000
   177 V      0.836         3.089 +- 0.926
   184 S      0.999**       3.498 +- 0.062
   215 T      0.976*        3.441 +- 0.379
   252 L      0.987*        3.466 +- 0.288
   254 D      0.859         3.148 +- 0.870
   256 T      0.949         3.373 +- 0.549
   268 E      1.000**       3.500 +- 0.002
   275 N      1.000**       3.500 +- 0.011
   283 H      1.000**       3.500 +- 0.018
   294 E      1.000**       3.500 +- 0.002
   302 E      1.000**       3.500 +- 0.025
   305 Y      1.000**       3.500 +- 0.030
   306 Q      1.000**       3.500 +- 0.000
   308 V      1.000**       3.500 +- 0.001
   309 E      1.000**       3.500 +- 0.002
   314 Q      0.996**       3.490 +- 0.156
   319 V      1.000**       3.500 +- 0.001
   321 D      1.000**       3.500 +- 0.003
   322 Q      0.997**       3.493 +- 0.132
   323 S      1.000**       3.500 +- 0.003
   348 Q      1.000**       3.500 +- 0.000
   378 S      1.000**       3.500 +- 0.002
   380 P      1.000**       3.500 +- 0.001
   384 T      1.000**       3.500 +- 0.003
   398 N      1.000**       3.500 +- 0.000
   399 N      1.000**       3.500 +- 0.000
   400 D      1.000**       3.500 +- 0.000
   401 T      1.000**       3.500 +- 0.002
   436 R      1.000**       3.500 +- 0.024
   542 A      0.998**       3.495 +- 0.117
   547 N      1.000**       3.500 +- 0.001
   554 L      1.000**       3.500 +- 0.000
   555 E      1.000**       3.500 +- 0.000
   556 Y      1.000**       3.500 +- 0.002
   564 Q      0.985*        3.462 +- 0.308
   570 D      0.983*        3.457 +- 0.325
   574 N      1.000**       3.500 +- 0.000
   575 L      0.985*        3.462 +- 0.305
   578 T      1.000**       3.500 +- 0.000
   608 D      0.998**       3.495 +- 0.117
   654 H      0.547         2.366 +- 1.245
   655 H      1.000**       3.500 +- 0.004
   657 A      0.978*        3.445 +- 0.365
   658 P      0.712         2.779 +- 1.132
   680 G      0.999**       3.499 +- 0.058
   684 N      0.549         2.371 +- 1.244
   720 A      0.998**       3.494 +- 0.124
   760 I      0.996**       3.490 +- 0.161
   761 V      0.990*        3.475 +- 0.250
   764 T      1.000**       3.500 +- 0.013
   765 Y      1.000**       3.500 +- 0.001
   769 L      0.998**       3.495 +- 0.115
   779 L      0.853         3.133 +- 0.885


Model 8 vs 7	1187.247940000001

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.GB.08.D650_E9.HQ595775_)

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

     7 R      1.000**       3.155
    10 H      0.995**       3.145
    14 T      0.667         2.414
    77 E      1.000**       3.156
   125 D      0.528         2.109
   126 N      1.000**       3.156
   127 S      1.000**       3.156
   128 S      1.000**       3.156
   129 E      1.000**       3.156
   130 E      1.000**       3.156
   131 R      1.000**       3.156
   132 G      1.000**       3.156
   149 Q      1.000**       3.155
   152 Y      0.942         3.026
   164 D      1.000**       3.156
   165 N      1.000**       3.156
   166 T      1.000**       3.156
   167 T      1.000**       3.156
   177 V      0.894         2.921
   184 S      1.000**       3.155
   215 T      0.977*        3.105
   252 L      0.990**       3.134
   254 D      0.877         2.884
   256 T      0.966*        3.081
   268 E      1.000**       3.156
   275 N      1.000**       3.156
   283 H      1.000**       3.156
   294 E      1.000**       3.156
   302 E      1.000**       3.156
   305 Y      1.000**       3.156
   306 Q      1.000**       3.156
   308 V      1.000**       3.156
   309 E      1.000**       3.156
   314 Q      0.997**       3.149
   319 V      1.000**       3.156
   321 D      1.000**       3.156
   322 Q      0.998**       3.151
   323 S      1.000**       3.156
   348 Q      1.000**       3.156
   378 S      1.000**       3.156
   380 P      1.000**       3.156
   384 T      1.000**       3.156
   398 N      1.000**       3.156
   399 N      1.000**       3.156
   400 D      1.000**       3.156
   401 T      1.000**       3.156
   436 R      1.000**       3.156
   542 A      0.998**       3.152
   547 N      1.000**       3.156
   554 L      1.000**       3.156
   555 E      1.000**       3.156
   556 Y      1.000**       3.156
   564 Q      0.988*        3.130
   570 D      0.985*        3.122
   574 N      1.000**       3.156
   575 L      0.988*        3.129
   578 T      1.000**       3.156
   608 D      0.998**       3.152
   654 H      0.656         2.385
   655 H      1.000**       3.156
   657 A      0.983*        3.119
   658 P      0.791         2.688
   680 G      0.999**       3.155
   684 N      0.613         2.295
   720 A      0.998**       3.153
   760 I      0.996**       3.148
   761 V      0.991**       3.136
   764 T      1.000**       3.156
   765 Y      1.000**       3.156
   769 L      0.999**       3.153
   779 L      0.885         2.900

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.GB.08.D650_E9.HQ595775_)

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

     7 R      0.999**       3.498 +- 0.079
    10 H      0.981*        3.451 +- 0.352
    77 E      1.000**       3.500 +- 0.000
   126 N      1.000**       3.500 +- 0.001
   127 S      1.000**       3.500 +- 0.000
   128 S      1.000**       3.500 +- 0.000
   129 E      1.000**       3.500 +- 0.000
   130 E      1.000**       3.500 +- 0.000
   131 R      1.000**       3.500 +- 0.000
   132 G      1.000**       3.500 +- 0.000
   149 Q      0.999**       3.497 +- 0.087
   152 Y      0.772         2.913 +- 1.080
   164 D      1.000**       3.500 +- 0.001
   165 N      1.000**       3.500 +- 0.000
   166 T      0.999**       3.498 +- 0.074
   167 T      1.000**       3.500 +- 0.000
   177 V      0.664         2.634 +- 1.219
   184 S      0.999**       3.498 +- 0.078
   215 T      0.889         3.215 +- 0.806
   252 L      0.974*        3.433 +- 0.411
   254 D      0.544         2.326 +- 1.281
   256 T      0.870         3.166 +- 0.865
   268 E      1.000**       3.500 +- 0.004
   275 N      1.000**       3.500 +- 0.017
   283 H      1.000**       3.500 +- 0.032
   294 E      1.000**       3.500 +- 0.003
   302 E      1.000**       3.499 +- 0.049
   305 Y      0.999**       3.499 +- 0.059
   306 Q      1.000**       3.500 +- 0.000
   308 V      1.000**       3.500 +- 0.001
   309 E      1.000**       3.500 +- 0.003
   314 Q      0.989*        3.472 +- 0.269
   319 V      1.000**       3.500 +- 0.001
   321 D      1.000**       3.500 +- 0.005
   322 Q      0.991**       3.477 +- 0.244
   323 S      1.000**       3.500 +- 0.003
   348 Q      1.000**       3.500 +- 0.000
   378 S      1.000**       3.500 +- 0.004
   380 P      1.000**       3.500 +- 0.001
   384 T      1.000**       3.500 +- 0.004
   398 N      1.000**       3.500 +- 0.000
   399 N      1.000**       3.500 +- 0.001
   400 D      1.000**       3.500 +- 0.000
   401 T      1.000**       3.500 +- 0.004
   436 R      1.000**       3.499 +- 0.038
   542 A      0.993**       3.483 +- 0.208
   547 N      1.000**       3.500 +- 0.001
   554 L      1.000**       3.500 +- 0.000
   555 E      1.000**       3.500 +- 0.000
   556 Y      1.000**       3.500 +- 0.003
   564 Q      0.958*        3.391 +- 0.518
   570 D      0.920         3.295 +- 0.695
   574 N      1.000**       3.500 +- 0.000
   575 L      0.951*        3.375 +- 0.553
   578 T      1.000**       3.500 +- 0.000
   608 D      0.991**       3.477 +- 0.241
   655 H      1.000**       3.500 +- 0.005
   657 A      0.932         3.326 +- 0.646
   680 G      0.998**       3.496 +- 0.107
   720 A      0.995**       3.488 +- 0.175
   760 I      0.984*        3.459 +- 0.321
   761 V      0.960*        3.398 +- 0.502
   764 T      1.000**       3.500 +- 0.021
   765 Y      1.000**       3.500 +- 0.001
   769 L      0.997**       3.491 +- 0.149
   779 L      0.630         2.546 +- 1.246