--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Mar 17 15:12:37 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -49724.95        -49772.04
2     -49725.94        -49766.57
--------------------------------------
TOTAL   -49725.33        -49771.35
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         8.462852    0.048676    8.059313    8.913363    8.458578   1088.13   1190.79    1.001
r(A<->C){all}   0.134779    0.000025    0.124888    0.144370    0.134708    381.13    420.20    1.002
r(A<->G){all}   0.298388    0.000096    0.279658    0.317868    0.298196    299.48    328.54    1.002
r(A<->T){all}   0.054721    0.000009    0.049071    0.060394    0.054632    506.28    537.13    1.000
r(C<->G){all}   0.079657    0.000026    0.070332    0.089950    0.079573    557.67    614.70    1.000
r(C<->T){all}   0.340936    0.000111    0.320068    0.360484    0.340866    319.88    328.08    1.003
r(G<->T){all}   0.091518    0.000022    0.082686    0.100737    0.091465    458.48    486.47    1.001
pi(A){all}      0.397717    0.000044    0.384921    0.410402    0.397990    423.01    437.26    1.000
pi(C){all}      0.173452    0.000023    0.164095    0.182634    0.173347    283.01    364.68    1.004
pi(G){all}      0.213848    0.000023    0.203784    0.222593    0.213859    636.69    639.63    1.007
pi(T){all}      0.214983    0.000032    0.203765    0.225667    0.214934    394.62    416.75    1.000
alpha{1,2}      0.483987    0.000525    0.440416    0.528128    0.482779   1041.00   1054.31    1.002
alpha{3}        1.058125    0.003776    0.945884    1.184467    1.058257   1163.56   1241.72    1.000
pinvar{all}     0.168000    0.000184    0.142712    0.196071    0.167635    978.20   1109.43    1.002
------------------------------------------------------------------------------------------------------
* 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	-41777.178034
Model 2: PositiveSelection	-41031.166056
Model 0: one-ratio	-44475.690467
Model 3: discrete	-40991.78024
Model 7: beta	-41552.440307
Model 8: beta&w>1	-40894.759678


Model 0 vs 1	5397.024866000007

Model 2 vs 1	1492.02395599999

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.10.DEMB10US011.KC473830_)

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

     8 C      0.967*        3.631
    69 E      1.000**       3.720
   115 E      1.000**       3.720
   116 T      1.000**       3.720
   117 N      1.000**       3.720
   118 T      1.000**       3.720
   119 T      1.000**       3.720
   120 N      1.000**       3.720
   121 A      1.000**       3.720
   122 T      1.000**       3.720
   123 A      1.000**       3.720
   134 D      0.984*        3.678
   150 K      0.981*        3.670
   153 G      0.998**       3.714
   154 N      1.000**       3.720
   155 T      1.000**       3.720
   174 S      0.999**       3.718
   205 N      0.993**       3.702
   245 A      0.940         3.558
   257 N      1.000**       3.720
   272 H      1.000**       3.720
   282 A      1.000**       3.720
   296 R      1.000**       3.720
   297 A      1.000**       3.720
   298 Q      1.000**       3.720
   301 N      1.000**       3.720
   304 Q      0.999**       3.718
   305 K      1.000**       3.720
   307 A      1.000**       3.720
   308 T      1.000**       3.719
   311 G      1.000**       3.720
   319 S      1.000**       3.720
   321 K      1.000**       3.720
   322 N      1.000**       3.720
   323 S      0.999**       3.717
   348 Q      1.000**       3.720
   352 R      1.000**       3.720
   353 S      1.000**       3.720
   354 D      1.000**       3.720
   381 K      0.998**       3.716
   383 L      1.000**       3.720
   401 N      1.000**       3.720
   402 D      1.000**       3.720
   403 T      1.000**       3.720
   404 L      1.000**       3.720
   546 N      1.000**       3.720
   551 N      0.992**       3.699
   557 L      1.000**       3.720
   558 S      1.000**       3.720
   559 D      1.000**       3.720
   578 S      1.000**       3.720
   579 I      1.000**       3.720
   582 T      1.000**       3.720
   589 N      0.981*        3.668
   612 D      1.000**       3.720
   659 L      1.000**       3.720
   661 A      1.000**       3.720
   662 P      1.000**       3.720
   684 E      1.000**       3.720
   688 D      0.995**       3.707
   694 F      1.000**       3.720
   718 R      0.998**       3.714
   723 L      0.784         3.133
   763 L      0.778         3.116
   764 V      1.000**       3.720
   767 I      1.000**       3.720
   768 C      1.000**       3.720
   772 C      1.000**       3.720
   782 A      1.000**       3.720
   787 V      0.559         2.522

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.10.DEMB10US011.KC473830_)

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

     8 C      0.973*        3.432 +- 0.408
    69 E      1.000**       3.500 +- 0.007
   115 E      1.000**       3.500 +- 0.000
   116 T      1.000**       3.500 +- 0.000
   117 N      1.000**       3.500 +- 0.001
   118 T      1.000**       3.500 +- 0.000
   119 T      1.000**       3.500 +- 0.000
   120 N      1.000**       3.500 +- 0.000
   121 A      1.000**       3.500 +- 0.000
   122 T      1.000**       3.500 +- 0.000
   123 A      1.000**       3.500 +- 0.000
   134 D      0.988*        3.471 +- 0.269
   150 K      0.986*        3.466 +- 0.290
   153 G      0.998**       3.496 +- 0.102
   154 N      1.000**       3.500 +- 0.001
   155 T      1.000**       3.500 +- 0.002
   165 V      0.503         2.258 +- 1.250
   174 S      0.999**       3.497 +- 0.080
   197 T      0.519         2.298 +- 1.249
   205 N      0.995**       3.487 +- 0.178
   245 A      0.956*        3.390 +- 0.512
   257 N      1.000**       3.500 +- 0.017
   264 N      0.536         2.340 +- 1.247
   272 H      1.000**       3.500 +- 0.007
   282 A      1.000**       3.500 +- 0.007
   296 R      1.000**       3.500 +- 0.001
   297 A      1.000**       3.500 +- 0.000
   298 Q      1.000**       3.500 +- 0.002
   301 N      1.000**       3.500 +- 0.004
   304 Q      0.999**       3.498 +- 0.065
   305 K      1.000**       3.500 +- 0.001
   307 A      1.000**       3.500 +- 0.001
   308 T      1.000**       3.499 +- 0.037
   311 G      1.000**       3.500 +- 0.013
   319 S      1.000**       3.500 +- 0.000
   321 K      1.000**       3.500 +- 0.003
   322 N      1.000**       3.500 +- 0.025
   323 S      0.999**       3.497 +- 0.092
   348 Q      1.000**       3.500 +- 0.003
   352 R      1.000**       3.500 +- 0.003
   353 S      1.000**       3.500 +- 0.000
   354 D      1.000**       3.500 +- 0.000
   381 K      0.999**       3.497 +- 0.085
   383 L      1.000**       3.500 +- 0.002
   401 N      1.000**       3.500 +- 0.001
   402 D      1.000**       3.500 +- 0.000
   403 T      1.000**       3.500 +- 0.000
   404 L      1.000**       3.500 +- 0.002
   546 N      1.000**       3.500 +- 0.001
   551 N      0.993**       3.483 +- 0.204
   557 L      1.000**       3.500 +- 0.000
   558 S      1.000**       3.500 +- 0.003
   559 D      1.000**       3.500 +- 0.000
   578 S      1.000**       3.500 +- 0.000
   579 I      1.000**       3.500 +- 0.004
   582 T      1.000**       3.500 +- 0.007
   589 N      0.986*        3.466 +- 0.291
   612 D      1.000**       3.500 +- 0.001
   659 L      1.000**       3.500 +- 0.016
   661 A      1.000**       3.500 +- 0.020
   662 P      1.000**       3.500 +- 0.007
   684 E      1.000**       3.500 +- 0.002
   688 D      0.997**       3.492 +- 0.145
   694 F      1.000**       3.500 +- 0.004
   718 R      0.997**       3.494 +- 0.126
   723 L      0.831         3.078 +- 0.937
   763 L      0.848         3.121 +- 0.897
   764 V      1.000**       3.500 +- 0.018
   767 I      1.000**       3.500 +- 0.008
   768 C      1.000**       3.500 +- 0.008
   772 C      1.000**       3.500 +- 0.011
   782 A      1.000**       3.500 +- 0.001
   787 V      0.657         2.641 +- 1.187


Model 8 vs 7	1315.36125799999

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.10.DEMB10US011.KC473830_)

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

     8 C      0.967*        3.144
    69 E      1.000**       3.219
   115 E      1.000**       3.219
   116 T      1.000**       3.219
   117 N      1.000**       3.219
   118 T      1.000**       3.219
   119 T      1.000**       3.219
   120 N      1.000**       3.219
   121 A      1.000**       3.219
   122 T      1.000**       3.219
   123 A      1.000**       3.219
   134 D      0.978*        3.170
   150 K      0.978*        3.169
   153 G      0.995**       3.209
   154 N      1.000**       3.219
   155 T      1.000**       3.219
   174 S      0.999**       3.217
   205 N      0.991**       3.198
   245 A      0.946         3.098
   257 N      1.000**       3.219
   272 H      1.000**       3.219
   282 A      1.000**       3.219
   296 R      1.000**       3.219
   297 A      1.000**       3.219
   298 Q      1.000**       3.219
   301 N      1.000**       3.219
   304 Q      0.998**       3.216
   305 K      1.000**       3.219
   307 A      1.000**       3.219
   308 T      1.000**       3.218
   311 G      1.000**       3.219
   319 S      1.000**       3.219
   321 K      1.000**       3.219
   322 N      1.000**       3.219
   323 S      0.999**       3.216
   348 Q      1.000**       3.219
   352 R      1.000**       3.219
   353 S      1.000**       3.219
   354 D      1.000**       3.219
   381 K      0.997**       3.213
   383 L      1.000**       3.219
   401 N      1.000**       3.219
   402 D      1.000**       3.219
   403 T      1.000**       3.219
   404 L      1.000**       3.219
   546 N      1.000**       3.219
   551 N      0.991**       3.199
   557 L      1.000**       3.219
   558 S      1.000**       3.219
   559 D      1.000**       3.219
   578 S      1.000**       3.219
   579 I      1.000**       3.219
   582 T      1.000**       3.219
   589 N      0.975*        3.163
   612 D      1.000**       3.219
   659 L      1.000**       3.219
   661 A      1.000**       3.219
   662 P      1.000**       3.219
   684 E      1.000**       3.219
   688 D      0.993**       3.203
   694 F      1.000**       3.219
   718 R      0.997**       3.213
   723 L      0.827         2.826
   763 L      0.756         2.667
   764 V      1.000**       3.219
   767 I      1.000**       3.219
   768 C      1.000**       3.219
   772 C      1.000**       3.219
   782 A      1.000**       3.219
   787 V      0.563         2.225

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.10.DEMB10US011.KC473830_)

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

     8 C      0.909         3.266 +- 0.740
    69 E      1.000**       3.500 +- 0.013
   115 E      1.000**       3.500 +- 0.001
   116 T      1.000**       3.500 +- 0.001
   117 N      1.000**       3.500 +- 0.001
   118 T      1.000**       3.500 +- 0.001
   119 T      1.000**       3.500 +- 0.001
   120 N      1.000**       3.500 +- 0.001
   121 A      1.000**       3.500 +- 0.001
   122 T      1.000**       3.500 +- 0.001
   123 A      1.000**       3.500 +- 0.001
   134 D      0.934         3.331 +- 0.636
   150 K      0.928         3.316 +- 0.662
   153 G      0.986*        3.465 +- 0.298
   154 N      1.000**       3.500 +- 0.002
   155 T      1.000**       3.500 +- 0.005
   174 S      0.998**       3.495 +- 0.114
   205 N      0.973*        3.430 +- 0.418
   245 A      0.838         3.084 +- 0.946
   257 N      1.000**       3.499 +- 0.044
   272 H      1.000**       3.500 +- 0.014
   282 A      1.000**       3.500 +- 0.015
   296 R      1.000**       3.500 +- 0.002
   297 A      1.000**       3.500 +- 0.001
   298 Q      1.000**       3.500 +- 0.005
   301 N      1.000**       3.500 +- 0.009
   304 Q      0.996**       3.490 +- 0.162
   305 K      1.000**       3.500 +- 0.001
   307 A      1.000**       3.500 +- 0.001
   308 T      0.999**       3.498 +- 0.080
   311 G      1.000**       3.500 +- 0.033
   319 S      1.000**       3.500 +- 0.001
   321 K      1.000**       3.500 +- 0.008
   322 N      0.999**       3.499 +- 0.059
   323 S      0.997**       3.493 +- 0.131
   348 Q      1.000**       3.500 +- 0.007
   352 R      1.000**       3.500 +- 0.009
   353 S      1.000**       3.500 +- 0.001
   354 D      1.000**       3.500 +- 0.001
   381 K      0.991**       3.477 +- 0.241
   383 L      1.000**       3.500 +- 0.003
   401 N      1.000**       3.500 +- 0.003
   402 D      1.000**       3.500 +- 0.001
   403 T      1.000**       3.500 +- 0.001
   404 L      1.000**       3.500 +- 0.004
   546 N      1.000**       3.500 +- 0.001
   551 N      0.976*        3.439 +- 0.391
   557 L      1.000**       3.500 +- 0.001
   558 S      1.000**       3.500 +- 0.008
   559 D      1.000**       3.500 +- 0.001
   578 S      1.000**       3.500 +- 0.001
   579 I      1.000**       3.500 +- 0.007
   582 T      1.000**       3.500 +- 0.014
   589 N      0.918         3.289 +- 0.705
   612 D      1.000**       3.500 +- 0.003
   659 L      1.000**       3.500 +- 0.023
   661 A      1.000**       3.500 +- 0.036
   662 P      1.000**       3.500 +- 0.009
   684 E      1.000**       3.500 +- 0.005
   688 D      0.977*        3.441 +- 0.385
   694 F      1.000**       3.500 +- 0.007
   718 R      0.994**       3.486 +- 0.191
   723 L      0.598         2.464 +- 1.264
   764 V      1.000**       3.499 +- 0.040
   767 I      1.000**       3.500 +- 0.013
   768 C      1.000**       3.500 +- 0.014
   772 C      1.000**       3.500 +- 0.015
   782 A      1.000**       3.500 +- 0.002