--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Jan 25 09:11:05 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -47535.55        -47579.59
2     -47533.27        -47573.31
--------------------------------------
TOTAL   -47533.87        -47578.89
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         8.147714    0.052385    7.729361    8.626980    8.139656   1076.76   1204.17    1.001
r(A<->C){all}   0.141654    0.000032    0.130391    0.152396    0.141447    401.70    411.87    1.000
r(A<->G){all}   0.291887    0.000102    0.272137    0.311162    0.291604    145.65    180.29    1.000
r(A<->T){all}   0.046725    0.000008    0.041422    0.052354    0.046612    323.12    464.97    1.000
r(C<->G){all}   0.075533    0.000024    0.066197    0.084946    0.075400    553.00    591.86    1.001
r(C<->T){all}   0.357902    0.000122    0.336487    0.379274    0.357698    160.72    168.28    1.000
r(G<->T){all}   0.086299    0.000022    0.076782    0.095107    0.086236    423.94    451.99    1.002
pi(A){all}      0.399936    0.000045    0.386726    0.412288    0.399934    290.39    292.73    1.000
pi(C){all}      0.165861    0.000024    0.156395    0.175030    0.165837    179.73    242.44    1.000
pi(G){all}      0.218510    0.000027    0.208984    0.228663    0.218562    292.20    298.88    1.000
pi(T){all}      0.215693    0.000035    0.204815    0.227487    0.215640    227.78    310.02    1.000
alpha{1,2}      0.477318    0.000529    0.433189    0.524312    0.476482    997.07   1084.58    1.000
alpha{3}        1.126482    0.004631    0.993516    1.259227    1.126366   1182.96   1268.03    1.000
pinvar{all}     0.195947    0.000190    0.169324    0.221458    0.195847   1151.71   1168.68    1.001
------------------------------------------------------------------------------------------------------
* 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	-39250.562022
Model 2: PositiveSelection	-38585.194973
Model 0: one-ratio	-41788.41876
Model 3: discrete	-38541.392658
Model 7: beta	-39026.033037
Model 8: beta&w>1	-38448.428616


Model 0 vs 1	5075.713476000004

Model 2 vs 1	1330.7340980000008

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.03.03ZAPS133MB1.DQ275646_)

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

     4 K      0.981*        3.536
     7 Q      0.846         3.186
    14 M      0.976*        3.523
    55 E      0.956*        3.471
    78 V      1.000**       3.584
   125 T      1.000**       3.584
   127 A      1.000**       3.584
   135 T      0.999**       3.581
   142 K      1.000**       3.583
   145 Y      0.559         2.445
   155 P      0.996**       3.573
   157 N      1.000**       3.584
   158 G      1.000**       3.584
   159 N      1.000**       3.584
   160 S      1.000**       3.584
   179 S      0.897         3.317
   246 L      0.878         3.268
   260 S      0.938         3.423
   262 Q      1.000**       3.584
   264 V      0.997**       3.577
   277 R      1.000**       3.584
   299 D      1.000**       3.584
   300 Q      0.998**       3.578
   303 R      0.745         2.925
   306 E      1.000**       3.584
   307 Q      1.000**       3.584
   309 K      1.000**       3.584
   310 K      1.000**       3.584
   313 G      1.000**       3.584
   315 H      0.999**       3.580
   319 L      1.000**       3.584
   321 A      1.000**       3.584
   322 P      0.987*        3.550
   323 A      1.000**       3.584
   348 N      1.000**       3.584
   351 K      1.000**       3.584
   352 S      1.000**       3.584
   353 D      1.000**       3.583
   354 E      1.000**       3.584
   382 E      1.000**       3.583
   384 N      1.000**       3.584
   386 T      0.680         2.756
   388 N      1.000**       3.584
   402 R      1.000**       3.584
   403 N      1.000**       3.583
   404 D      1.000**       3.584
   405 T      1.000**       3.584
   440 T      0.796         3.058
   544 A      1.000**       3.583
   549 S      1.000**       3.583
   555 Q      1.000**       3.584
   556 T      1.000**       3.584
   557 D      1.000**       3.583
   560 D      1.000**       3.584
   572 N      0.872         3.252
   576 G      1.000**       3.584
   577 T      1.000**       3.584
   580 R      1.000**       3.584
   610 D      0.987*        3.551
   657 T      1.000**       3.584
   659 N      1.000**       3.583
   660 P      0.995**       3.570
   682 V      1.000**       3.583
   686 S      0.959*        3.477
   692 A      1.000**       3.584
   719 H      0.999**       3.582
   724 A      1.000**       3.583
   733 Q      0.868         3.241
   760 V      0.991**       3.560
   761 I      0.855         3.209
   764 I      0.990*        3.557
   765 C      1.000**       3.584
   769 S      1.000**       3.584
   779 F      0.985*        3.545

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.03.03ZAPS133MB1.DQ275646_)

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

     4 K      0.981*        3.454 +- 0.338
     7 Q      0.845         3.112 +- 0.905
    14 M      0.975*        3.438 +- 0.388
    55 E      0.957*        3.392 +- 0.508
    78 V      1.000**       3.500 +- 0.001
   125 T      1.000**       3.500 +- 0.012
   127 A      1.000**       3.500 +- 0.000
   135 T      0.999**       3.498 +- 0.078
   142 K      1.000**       3.499 +- 0.050
   145 Y      0.581         2.452 +- 1.234
   155 P      0.995**       3.489 +- 0.168
   157 N      1.000**       3.500 +- 0.007
   158 G      1.000**       3.500 +- 0.000
   159 N      1.000**       3.500 +- 0.001
   160 S      1.000**       3.500 +- 0.000
   179 S      0.892         3.229 +- 0.777
   246 L      0.870         3.176 +- 0.839
   260 S      0.935         3.338 +- 0.615
   262 Q      1.000**       3.500 +- 0.005
   264 V      0.997**       3.493 +- 0.133
   277 R      1.000**       3.500 +- 0.001
   299 D      1.000**       3.500 +- 0.000
   300 Q      0.998**       3.495 +- 0.114
   303 R      0.763         2.909 +- 1.062
   306 E      1.000**       3.500 +- 0.000
   307 Q      1.000**       3.500 +- 0.000
   309 K      1.000**       3.500 +- 0.000
   310 K      1.000**       3.500 +- 0.000
   313 G      1.000**       3.500 +- 0.018
   315 H      0.999**       3.497 +- 0.093
   319 L      1.000**       3.500 +- 0.000
   321 A      1.000**       3.500 +- 0.006
   322 P      0.986*        3.466 +- 0.290
   323 A      1.000**       3.500 +- 0.007
   348 N      1.000**       3.500 +- 0.001
   351 K      1.000**       3.500 +- 0.000
   352 S      1.000**       3.500 +- 0.000
   353 D      1.000**       3.499 +- 0.043
   354 E      1.000**       3.500 +- 0.000
   382 E      1.000**       3.500 +- 0.026
   384 N      1.000**       3.500 +- 0.000
   386 T      0.702         2.756 +- 1.143
   388 N      1.000**       3.500 +- 0.011
   402 R      1.000**       3.500 +- 0.000
   403 N      1.000**       3.500 +- 0.031
   404 D      1.000**       3.500 +- 0.000
   405 T      1.000**       3.500 +- 0.004
   440 T      0.806         3.015 +- 0.989
   544 A      1.000**       3.500 +- 0.020
   549 S      1.000**       3.499 +- 0.045
   555 Q      1.000**       3.500 +- 0.000
   556 T      1.000**       3.500 +- 0.000
   557 D      1.000**       3.499 +- 0.043
   560 D      1.000**       3.500 +- 0.010
   572 N      0.879         3.197 +- 0.816
   576 G      1.000**       3.500 +- 0.000
   577 T      1.000**       3.500 +- 0.001
   580 R      1.000**       3.500 +- 0.000
   610 D      0.987*        3.468 +- 0.279
   657 T      1.000**       3.500 +- 0.000
   659 N      1.000**       3.500 +- 0.034
   660 P      0.994**       3.485 +- 0.191
   682 V      1.000**       3.499 +- 0.050
   686 S      0.959*        3.397 +- 0.496
   692 A      1.000**       3.500 +- 0.013
   719 H      0.999**       3.498 +- 0.073
   724 A      1.000**       3.499 +- 0.051
   733 Q      0.860         3.151 +- 0.867
   760 V      0.990**       3.476 +- 0.243
   761 I      0.858         3.145 +- 0.872
   764 I      0.989*        3.473 +- 0.260
   765 C      1.000**       3.500 +- 0.000
   769 S      1.000**       3.500 +- 0.014
   779 F      0.984*        3.460 +- 0.313


Model 8 vs 7	1155.2088420000073

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.03.03ZAPS133MB1.DQ275646_)

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

     4 K      0.977*        3.015
     7 Q      0.850         2.744
    14 M      0.975*        3.010
    55 E      0.949         2.954
    78 V      1.000**       3.062
   125 T      1.000**       3.062
   127 A      1.000**       3.062
   135 T      0.998**       3.059
   142 K      0.999**       3.061
   145 Y      0.605         2.223
   155 P      0.994**       3.050
   157 N      1.000**       3.062
   158 G      1.000**       3.062
   159 N      1.000**       3.062
   160 S      1.000**       3.062
   179 S      0.916         2.884
   246 L      0.887         2.821
   260 S      0.945         2.946
   262 Q      1.000**       3.062
   264 V      0.995**       3.051
   277 R      1.000**       3.062
   299 D      1.000**       3.062
   300 Q      0.996**       3.054
   303 R      0.721         2.474
   306 E      1.000**       3.062
   307 Q      1.000**       3.062
   309 K      1.000**       3.062
   310 K      1.000**       3.062
   313 G      1.000**       3.062
   315 H      0.998**       3.059
   319 L      1.000**       3.062
   321 A      1.000**       3.062
   322 P      0.984*        3.028
   323 A      1.000**       3.062
   348 N      1.000**       3.062
   351 K      1.000**       3.062
   352 S      1.000**       3.062
   353 D      0.999**       3.061
   354 E      1.000**       3.062
   382 E      1.000**       3.062
   384 N      1.000**       3.062
   386 T      0.647         2.316
   388 N      1.000**       3.062
   402 R      1.000**       3.062
   403 N      1.000**       3.062
   404 D      1.000**       3.062
   405 T      1.000**       3.062
   440 T      0.801         2.641
   544 A      1.000**       3.062
   549 S      1.000**       3.062
   555 Q      1.000**       3.062
   556 T      1.000**       3.062
   557 D      0.999**       3.061
   560 D      1.000**       3.062
   572 N      0.856         2.758
   576 G      1.000**       3.062
   577 T      1.000**       3.062
   580 R      1.000**       3.062
   610 D      0.983*        3.027
   657 T      1.000**       3.062
   659 N      1.000**       3.062
   660 P      0.994**       3.050
   682 V      0.999**       3.061
   686 S      0.953*        2.962
   692 A      1.000**       3.062
   719 H      0.999**       3.060
   724 A      1.000**       3.061
   733 Q      0.867         2.778
   760 V      0.988*        3.038
   761 I      0.845         2.736
   764 I      0.988*        3.037
   765 C      1.000**       3.062
   769 S      1.000**       3.062
   779 F      0.981*        3.022

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.03.03ZAPS133MB1.DQ275646_)

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

     4 K      0.841         3.092 +- 0.936
    14 M      0.865         3.155 +- 0.874
    55 E      0.681         2.682 +- 1.193
    78 V      1.000**       3.499 +- 0.023
   125 T      1.000**       3.499 +- 0.038
   127 A      1.000**       3.499 +- 0.023
   135 T      0.989*        3.471 +- 0.271
   142 K      0.995**       3.487 +- 0.178
   155 P      0.967*        3.415 +- 0.458
   157 N      1.000**       3.499 +- 0.034
   158 G      1.000**       3.499 +- 0.023
   159 N      1.000**       3.499 +- 0.023
   160 S      1.000**       3.499 +- 0.023
   179 S      0.680         2.678 +- 1.198
   246 L      0.620         2.524 +- 1.247
   260 S      0.745         2.844 +- 1.118
   262 Q      1.000**       3.499 +- 0.027
   264 V      0.967*        3.415 +- 0.458
   277 R      1.000**       3.499 +- 0.023
   299 D      1.000**       3.499 +- 0.023
   300 Q      0.975*        3.436 +- 0.399
   306 E      1.000**       3.499 +- 0.023
   307 Q      1.000**       3.499 +- 0.023
   309 K      1.000**       3.499 +- 0.023
   310 K      1.000**       3.499 +- 0.023
   313 G      1.000**       3.498 +- 0.056
   315 H      0.993**       3.481 +- 0.217
   319 L      1.000**       3.499 +- 0.023
   321 A      1.000**       3.499 +- 0.029
   322 P      0.904         3.254 +- 0.754
   323 A      1.000**       3.499 +- 0.025
   348 N      1.000**       3.499 +- 0.023
   351 K      1.000**       3.499 +- 0.023
   352 S      1.000**       3.499 +- 0.023
   353 D      0.996**       3.489 +- 0.167
   354 E      1.000**       3.499 +- 0.023
   382 E      0.999**       3.497 +- 0.084
   384 N      1.000**       3.499 +- 0.023
   388 N      1.000**       3.499 +- 0.035
   402 R      1.000**       3.499 +- 0.023
   403 N      0.999**       3.496 +- 0.097
   404 D      1.000**       3.499 +- 0.023
   405 T      1.000**       3.499 +- 0.025
   544 A      1.000**       3.499 +- 0.049
   549 S      0.999**       3.497 +- 0.090
   555 Q      1.000**       3.499 +- 0.023
   556 T      1.000**       3.499 +- 0.023
   557 D      0.997**       3.493 +- 0.130
   560 D      1.000**       3.499 +- 0.043
   576 G      1.000**       3.499 +- 0.023
   577 T      1.000**       3.499 +- 0.023
   580 R      1.000**       3.499 +- 0.023
   610 D      0.875         3.180 +- 0.845
   657 T      1.000**       3.499 +- 0.023
   659 N      0.999**       3.498 +- 0.074
   660 P      0.979*        3.446 +- 0.367
   682 V      0.997**       3.493 +- 0.134
   686 S      0.702         2.736 +- 1.171
   692 A      1.000**       3.499 +- 0.033
   719 H      0.997**       3.493 +- 0.132
   724 A      0.999**       3.496 +- 0.095
   733 Q      0.561         2.371 +- 1.275
   760 V      0.929         3.318 +- 0.656
   764 I      0.928         3.315 +- 0.661
   765 C      1.000**       3.499 +- 0.023
   769 S      1.000**       3.499 +- 0.032
   779 F      0.903         3.251 +- 0.758