--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Jan 23 23:07:50 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -46829.37        -46875.01
2     -46826.96        -46876.45
--------------------------------------
TOTAL   -46827.56        -46875.97
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/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}         7.835093    0.048588    7.388076    8.258520    7.824838    522.49    825.16    1.000
r(A<->C){all}   0.145315    0.000033    0.133576    0.156111    0.145293    292.97    387.22    1.002
r(A<->G){all}   0.265284    0.000129    0.242404    0.285663    0.265236    140.54    164.14    1.001
r(A<->T){all}   0.049455    0.000008    0.043833    0.054798    0.049446    496.19    531.48    1.001
r(C<->G){all}   0.072205    0.000027    0.062387    0.082184    0.072172    564.30    571.35    1.000
r(C<->T){all}   0.383739    0.000164    0.358880    0.407808    0.383664    156.16    170.13    1.002
r(G<->T){all}   0.084002    0.000021    0.075477    0.093131    0.083938    330.98    390.68    1.000
pi(A){all}      0.400853    0.000044    0.386580    0.412449    0.400805    448.81    451.16    1.000
pi(C){all}      0.155870    0.000023    0.146719    0.165009    0.155762    260.32    329.84    1.000
pi(G){all}      0.230024    0.000044    0.216906    0.242461    0.230151    151.41    191.22    1.000
pi(T){all}      0.213254    0.000038    0.200874    0.224933    0.213144    303.53    310.06    1.000
alpha{1,2}      0.455799    0.000507    0.412984    0.500649    0.454861    671.52    726.63    1.001
alpha{3}        1.000879    0.003938    0.879968    1.121255    0.997946    982.20   1080.37    1.000
pinvar{all}     0.182920    0.000234    0.151893    0.211025    0.182903    889.89    898.39    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	-39499.780509
Model 2: PositiveSelection	-38800.288381
Model 0: one-ratio	-42177.068401
Model 3: discrete	-38772.241635
Model 7: beta	-39306.355662
Model 8: beta&w>1	-38679.867436


Model 0 vs 1	5354.575784000001

Model 2 vs 1	1398.984255999996

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.CAP327.2.00_C6.37.KF114885_)

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

     7 L      1.000**       3.633
    10 W      1.000**       3.633
    12 Q      0.990**       3.607
    24 N      0.566         2.490
    76 V      1.000**       3.633
   122 T      1.000**       3.633
   124 A      1.000**       3.633
   125 N      1.000**       3.633
   126 L      1.000**       3.633
   127 K      1.000**       3.633
   128 E      1.000**       3.633
   141 Q      1.000**       3.633
   143 Y      0.776         3.043
   153 P      0.883         3.325
   155 N      0.999**       3.630
   156 Y      1.000**       3.633
   157 S      1.000**       3.633
   158 E      1.000**       3.633
   177 T      0.990**       3.608
   208 H      0.994**       3.617
   245 L      0.928         3.445
   247 D      0.703         2.852
   249 A      0.980*        3.582
   259 S      0.946         3.490
   261 E      0.977*        3.573
   268 D      1.000**       3.633
   286 N      0.999**       3.632
   300 K      0.998**       3.628
   301 G      1.000**       3.633
   305 T      0.983*        3.589
   308 K      1.000**       3.633
   309 R      1.000**       3.633
   311 E      0.979*        3.579
   312 K      1.000**       3.633
   315 K      0.999**       3.631
   322 N      1.000**       3.633
   324 A      1.000**       3.633
   325 P      1.000**       3.633
   326 P      1.000**       3.633
   351 E      1.000**       3.633
   355 T      0.665         2.752
   356 S      1.000**       3.633
   357 E      1.000**       3.633
   358 L      1.000**       3.633
   360 K      1.000**       3.633
   361 T      0.999**       3.632
   377 E      0.985*        3.593
   388 A      1.000**       3.633
   394 V      1.000**       3.633
   408 N      1.000**       3.633
   409 N      1.000**       3.633
   410 N      1.000**       3.633
   411 N      1.000**       3.633
   412 N      1.000**       3.633
   447 Q      1.000**       3.633
   553 N      1.000**       3.633
   558 S      0.999**       3.632
   565 D      1.000**       3.633
   568 D      1.000**       3.633
   584 D      1.000**       3.633
   588 K      1.000**       3.633
   618 D      1.000**       3.633
   665 I      1.000**       3.633
   667 N      0.767         3.020
   668 P      0.996**       3.623
   687 N      0.920         3.422
   690 I      1.000**       3.633
   691 R      0.585         2.539
   694 N      0.981*        3.583
   700 A      0.988*        3.602
   714 Q      0.999**       3.630
   732 A      1.000**       3.633
   776 I      1.000**       3.633
   777 C      1.000**       3.633
   781 L      1.000**       3.633
   791 F      0.639         2.683

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.CAP327.2.00_C6.37.KF114885_)

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

     7 L      1.000**       3.499 +- 0.038
    10 W      1.000**       3.500 +- 0.000
    12 Q      0.991**       3.479 +- 0.231
    24 N      0.659         2.647 +- 1.185
    76 V      1.000**       3.500 +- 0.005
   122 T      1.000**       3.500 +- 0.017
   124 A      1.000**       3.500 +- 0.000
   125 N      1.000**       3.500 +- 0.000
   126 L      1.000**       3.500 +- 0.000
   127 K      1.000**       3.500 +- 0.000
   128 E      1.000**       3.499 +- 0.041
   141 Q      1.000**       3.500 +- 0.011
   143 Y      0.823         3.058 +- 0.954
   153 P      0.913         3.283 +- 0.704
   155 N      0.999**       3.497 +- 0.087
   156 Y      1.000**       3.500 +- 0.000
   157 S      1.000**       3.500 +- 0.001
   158 E      1.000**       3.500 +- 0.000
   177 T      0.991**       3.477 +- 0.237
   208 H      0.995**       3.487 +- 0.182
   245 L      0.937         3.343 +- 0.606
   247 D      0.776         2.939 +- 1.043
   249 A      0.984*        3.460 +- 0.315
   259 S      0.955*        3.387 +- 0.519
   261 E      0.984*        3.460 +- 0.315
   268 D      1.000**       3.500 +- 0.004
   286 N      1.000**       3.499 +- 0.051
   300 K      0.999**       3.496 +- 0.096
   301 G      1.000**       3.500 +- 0.000
   305 T      0.987*        3.468 +- 0.281
   308 K      1.000**       3.500 +- 0.014
   309 R      1.000**       3.500 +- 0.028
   311 E      0.983*        3.458 +- 0.320
   312 K      1.000**       3.500 +- 0.004
   315 K      0.999**       3.498 +- 0.070
   322 N      1.000**       3.500 +- 0.001
   324 A      1.000**       3.500 +- 0.003
   325 P      1.000**       3.500 +- 0.003
   326 P      1.000**       3.499 +- 0.038
   351 E      1.000**       3.500 +- 0.001
   355 T      0.754         2.886 +- 1.076
   356 S      1.000**       3.500 +- 0.000
   357 E      1.000**       3.500 +- 0.000
   358 L      1.000**       3.500 +- 0.000
   360 K      1.000**       3.500 +- 0.000
   361 T      0.999**       3.499 +- 0.056
   377 E      0.989*        3.471 +- 0.266
   388 A      1.000**       3.500 +- 0.017
   394 V      1.000**       3.500 +- 0.002
   408 N      1.000**       3.500 +- 0.000
   409 N      1.000**       3.500 +- 0.000
   410 N      1.000**       3.500 +- 0.000
   411 N      1.000**       3.500 +- 0.000
   412 N      1.000**       3.500 +- 0.002
   447 Q      1.000**       3.500 +- 0.024
   534 K      0.506         2.265 +- 1.250
   553 N      1.000**       3.500 +- 0.000
   558 S      0.999**       3.499 +- 0.058
   565 D      1.000**       3.500 +- 0.000
   568 D      1.000**       3.500 +- 0.003
   584 D      1.000**       3.500 +- 0.000
   588 K      1.000**       3.499 +- 0.041
   618 D      1.000**       3.500 +- 0.000
   665 I      1.000**       3.500 +- 0.015
   667 N      0.817         3.044 +- 0.966
   668 P      0.996**       3.491 +- 0.154
   687 N      0.939         3.349 +- 0.596
   690 I      1.000**       3.500 +- 0.012
   691 R      0.626         2.566 +- 1.209
   694 N      0.985*        3.463 +- 0.302
   700 A      0.989*        3.474 +- 0.256
   714 Q      0.999**       3.497 +- 0.090
   732 A      1.000**       3.500 +- 0.015
   776 I      1.000**       3.500 +- 0.033
   777 C      1.000**       3.500 +- 0.000
   781 L      1.000**       3.500 +- 0.005
   791 F      0.698         2.746 +- 1.148


Model 8 vs 7	1252.9764520000026

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.CAP327.2.00_C6.37.KF114885_)

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

     7 L      1.000**       3.159
    10 W      1.000**       3.160
    12 Q      0.989*        3.136
    24 N      0.595         2.264
    76 V      1.000**       3.159
   122 T      1.000**       3.159
   124 A      1.000**       3.160
   125 N      1.000**       3.160
   126 L      1.000**       3.160
   127 K      1.000**       3.160
   128 E      0.999**       3.158
   141 Q      1.000**       3.159
   143 Y      0.805         2.726
   153 P      0.892         2.922
   155 N      0.998**       3.154
   156 Y      1.000**       3.160
   157 S      1.000**       3.160
   158 E      1.000**       3.160
   177 T      0.991**       3.140
   208 H      0.993**       3.143
   245 L      0.933         3.011
   247 D      0.709         2.518
   249 A      0.983*        3.122
   259 S      0.954*        3.058
   261 E      0.972*        3.097
   268 D      1.000**       3.160
   286 N      0.999**       3.158
   300 K      0.997**       3.153
   301 G      1.000**       3.160
   305 T      0.980*        3.114
   308 K      1.000**       3.159
   309 R      1.000**       3.159
   311 E      0.979*        3.113
   312 K      1.000**       3.159
   315 K      0.998**       3.156
   322 N      1.000**       3.160
   324 A      1.000**       3.160
   325 P      1.000**       3.160
   326 P      1.000**       3.159
   351 E      1.000**       3.160
   355 T      0.671         2.433
   356 S      1.000**       3.160
   357 E      1.000**       3.160
   358 L      1.000**       3.160
   360 K      1.000**       3.160
   361 T      0.999**       3.158
   377 E      0.983*        3.122
   388 A      1.000**       3.159
   394 V      1.000**       3.160
   408 N      1.000**       3.160
   409 N      1.000**       3.160
   410 N      1.000**       3.160
   411 N      1.000**       3.160
   412 N      1.000**       3.160
   447 Q      1.000**       3.159
   553 N      1.000**       3.160
   558 S      0.999**       3.158
   565 D      1.000**       3.160
   568 D      1.000**       3.160
   584 D      1.000**       3.160
   588 K      1.000**       3.159
   618 D      1.000**       3.160
   665 I      1.000**       3.159
   667 N      0.800         2.718
   668 P      0.996**       3.151
   687 N      0.925         2.994
   690 I      1.000**       3.159
   691 R      0.582         2.222
   694 N      0.978*        3.111
   700 A      0.989*        3.135
   714 Q      0.999**       3.156
   732 A      1.000**       3.159
   776 I      1.000**       3.159
   777 C      1.000**       3.160
   781 L      1.000**       3.160
   791 F      0.614         2.296

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.CAP327.2.00_C6.37.KF114885_)

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

     7 L      0.999**       3.498 +- 0.070
    10 W      1.000**       3.500 +- 0.001
    12 Q      0.962*        3.404 +- 0.487
    76 V      1.000**       3.500 +- 0.010
   122 T      1.000**       3.499 +- 0.039
   124 A      1.000**       3.500 +- 0.000
   125 N      1.000**       3.500 +- 0.000
   126 L      1.000**       3.500 +- 0.000
   127 K      1.000**       3.500 +- 0.000
   128 E      0.998**       3.494 +- 0.120
   141 Q      1.000**       3.500 +- 0.016
   153 P      0.598         2.471 +- 1.255
   155 N      0.990**       3.475 +- 0.251
   156 Y      1.000**       3.500 +- 0.000
   157 S      1.000**       3.500 +- 0.003
   158 E      1.000**       3.500 +- 0.000
   177 T      0.976*        3.438 +- 0.394
   208 H      0.974*        3.433 +- 0.407
   245 L      0.805         3.000 +- 1.016
   249 A      0.934         3.331 +- 0.635
   259 S      0.842         3.094 +- 0.936
   261 E      0.853         3.124 +- 0.905
   268 D      1.000**       3.500 +- 0.007
   286 N      0.997**       3.492 +- 0.141
   300 K      0.987*        3.466 +- 0.292
   301 G      1.000**       3.500 +- 0.000
   305 T      0.907         3.263 +- 0.742
   308 K      1.000**       3.500 +- 0.033
   309 R      1.000**       3.499 +- 0.053
   311 E      0.916         3.284 +- 0.711
   312 K      1.000**       3.500 +- 0.010
   315 K      0.994**       3.484 +- 0.198
   322 N      1.000**       3.500 +- 0.002
   324 A      1.000**       3.500 +- 0.007
   325 P      1.000**       3.500 +- 0.005
   326 P      1.000**       3.499 +- 0.052
   351 E      1.000**       3.500 +- 0.002
   356 S      1.000**       3.500 +- 0.000
   357 E      1.000**       3.500 +- 0.000
   358 L      1.000**       3.500 +- 0.000
   360 K      1.000**       3.500 +- 0.000
   361 T      0.998**       3.494 +- 0.123
   377 E      0.917         3.288 +- 0.704
   388 A      1.000**       3.499 +- 0.042
   394 V      1.000**       3.500 +- 0.005
   408 N      1.000**       3.500 +- 0.000
   409 N      1.000**       3.500 +- 0.000
   410 N      1.000**       3.500 +- 0.000
   411 N      1.000**       3.500 +- 0.000
   412 N      1.000**       3.500 +- 0.004
   447 Q      1.000**       3.499 +- 0.055
   553 N      1.000**       3.500 +- 0.000
   558 S      0.998**       3.496 +- 0.103
   565 D      1.000**       3.500 +- 0.001
   568 D      1.000**       3.500 +- 0.007
   584 D      1.000**       3.500 +- 0.000
   588 K      0.999**       3.497 +- 0.086
   618 D      1.000**       3.500 +- 0.001
   665 I      1.000**       3.500 +- 0.022
   668 P      0.989*        3.473 +- 0.264
   687 N      0.699         2.730 +- 1.174
   690 I      1.000**       3.500 +- 0.026
   694 N      0.903         3.251 +- 0.758
   700 A      0.965*        3.411 +- 0.469
   714 Q      0.997**       3.492 +- 0.145
   732 A      1.000**       3.500 +- 0.023
   776 I      0.999**       3.498 +- 0.071
   777 C      1.000**       3.500 +- 0.001
   781 L      1.000**       3.500 +- 0.006