--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Mar 16 18:08:41 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -49062.58        -49102.16
2     -49062.60        -49097.89
--------------------------------------
TOTAL   -49062.59        -49101.48
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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}         8.327723    0.062764    7.838347    8.804613    8.323195    721.09    782.54    1.000
r(A<->C){all}   0.142434    0.000028    0.132260    0.152749    0.142495    379.58    487.51    1.001
r(A<->G){all}   0.284031    0.000124    0.262610    0.305678    0.283619    280.03    282.84    1.002
r(A<->T){all}   0.059054    0.000010    0.052999    0.065212    0.059008    482.02    509.82    1.003
r(C<->G){all}   0.074755    0.000026    0.064612    0.084583    0.074759    350.18    419.03    1.000
r(C<->T){all}   0.356884    0.000145    0.331768    0.379038    0.356876    287.44    299.18    1.003
r(G<->T){all}   0.082843    0.000021    0.073204    0.091287    0.082788    479.90    502.08    1.001
pi(A){all}      0.399460    0.000049    0.386136    0.413828    0.399375    291.57    366.11    1.006
pi(C){all}      0.164734    0.000025    0.155195    0.174894    0.164822    281.30    326.58    1.002
pi(G){all}      0.227160    0.000032    0.215584    0.237721    0.227137    362.23    394.57    1.000
pi(T){all}      0.208646    0.000034    0.196991    0.219576    0.208743    285.37    297.72    1.001
alpha{1,2}      0.474740    0.000535    0.432417    0.519954    0.473873    921.21   1003.63    1.000
alpha{3}        1.069343    0.004589    0.944083    1.203141    1.066979   1073.09   1089.85    1.000
pinvar{all}     0.173860    0.000209    0.145213    0.200875    0.174249   1111.26   1177.50    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	-40099.699125
Model 2: PositiveSelection	-39449.807234
Model 0: one-ratio	-42578.476225
Model 3: discrete	-39424.72764
Model 7: beta	-39913.947239
Model 8: beta&w>1	-39331.455117


Model 0 vs 1	4957.554199999999

Model 2 vs 1	1299.7837819999986

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.04.USPI71101EI7y04051pcWG2B9.JN024210_)

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

    51 A      0.766         2.981
    74 K      1.000**       3.585
   123 L      1.000**       3.585
   124 E      1.000**       3.585
   125 N      1.000**       3.585
   126 T      1.000**       3.585
   127 T      1.000**       3.585
   128 N      1.000**       3.585
   129 A      1.000**       3.585
   130 A      1.000**       3.585
   139 V      0.998**       3.580
   146 M      0.996**       3.575
   147 K      0.678         2.753
   150 Y      0.995**       3.572
   162 E      1.000**       3.585
   163 D      1.000**       3.585
   164 D      1.000**       3.585
   174 I      0.954*        3.465
   183 T      0.999**       3.582
   214 R      0.814         3.104
   251 K      0.982*        3.539
   253 T      1.000**       3.585
   265 V      0.991**       3.562
   272 N      1.000**       3.585
   280 H      0.995**       3.572
   289 E      1.000**       3.585
   296 Q      0.706         2.826
   305 K      1.000**       3.584
   308 E      0.976*        3.522
   309 K      1.000**       3.585
   311 V      1.000**       3.585
   312 E      1.000**       3.585
   315 R      0.998**       3.581
   322 T      1.000**       3.585
   324 K      0.998**       3.581
   325 P      0.991**       3.561
   326 S      1.000**       3.585
   351 Q      1.000**       3.585
   355 S      0.998**       3.579
   357 D      1.000**       3.585
   358 T      0.855         3.211
   385 R      1.000**       3.585
   387 Q      1.000**       3.585
   391 S      0.765         2.978
   405 V      1.000**       3.585
   406 N      1.000**       3.585
   407 T      1.000**       3.585
   408 T      1.000**       3.585
   443 K      1.000**       3.585
   459 V      0.890         3.300
   548 A      1.000**       3.585
   553 A      1.000**       3.585
   560 Q      1.000**       3.585
   561 K      1.000**       3.585
   562 Y      1.000**       3.585
   580 D      1.000**       3.585
   581 L      1.000**       3.585
   584 N      1.000**       3.585
   614 S      1.000**       3.585
   661 L      1.000**       3.585
   663 T      0.999**       3.583
   686 G      1.000**       3.585
   690 N      0.646         2.671
   696 V      0.832         3.150
   728 I      1.000**       3.585
   751 L      0.700         2.808
   772 V      1.000**       3.584
   773 F      1.000**       3.585
   779 L      0.513         2.326

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.04.USPI71101EI7y04051pcWG2B9.JN024210_)

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

    51 A      0.793         2.982 +- 1.013
    74 K      1.000**       3.500 +- 0.001
   123 L      1.000**       3.500 +- 0.000
   124 E      1.000**       3.500 +- 0.000
   125 N      1.000**       3.500 +- 0.000
   126 T      1.000**       3.500 +- 0.000
   127 T      1.000**       3.500 +- 0.000
   128 N      1.000**       3.500 +- 0.000
   129 A      1.000**       3.500 +- 0.000
   130 A      1.000**       3.500 +- 0.000
   139 V      0.998**       3.495 +- 0.109
   146 M      0.996**       3.491 +- 0.151
   147 K      0.681         2.704 +- 1.165
   150 Y      0.995**       3.488 +- 0.176
   162 E      1.000**       3.500 +- 0.001
   163 D      1.000**       3.500 +- 0.000
   164 D      1.000**       3.500 +- 0.013
   174 I      0.954*        3.385 +- 0.524
   183 T      0.999**       3.497 +- 0.090
   214 R      0.833         3.082 +- 0.933
   251 K      0.983*        3.458 +- 0.322
   253 T      1.000**       3.500 +- 0.006
   265 V      0.992**       3.480 +- 0.224
   272 N      1.000**       3.500 +- 0.000
   280 H      0.995**       3.488 +- 0.173
   289 E      1.000**       3.500 +- 0.000
   296 Q      0.725         2.813 +- 1.116
   305 K      1.000**       3.499 +- 0.038
   308 E      0.977*        3.443 +- 0.373
   309 K      1.000**       3.500 +- 0.000
   311 V      1.000**       3.500 +- 0.009
   312 E      1.000**       3.500 +- 0.005
   315 R      0.999**       3.496 +- 0.096
   322 T      1.000**       3.500 +- 0.000
   324 K      0.998**       3.496 +- 0.098
   325 P      0.991**       3.478 +- 0.235
   326 S      1.000**       3.500 +- 0.011
   351 Q      1.000**       3.500 +- 0.000
   355 S      0.998**       3.495 +- 0.112
   357 D      1.000**       3.500 +- 0.000
   358 T      0.865         3.162 +- 0.854
   385 R      1.000**       3.500 +- 0.022
   387 Q      1.000**       3.500 +- 0.000
   391 S      0.785         2.963 +- 1.027
   405 V      1.000**       3.500 +- 0.000
   406 N      1.000**       3.500 +- 0.001
   407 T      1.000**       3.500 +- 0.001
   408 T      1.000**       3.500 +- 0.000
   443 K      1.000**       3.500 +- 0.001
   459 V      0.896         3.239 +- 0.764
   548 A      1.000**       3.500 +- 0.011
   553 A      1.000**       3.500 +- 0.019
   560 Q      1.000**       3.500 +- 0.000
   561 K      1.000**       3.500 +- 0.001
   562 Y      1.000**       3.500 +- 0.013
   580 D      1.000**       3.500 +- 0.000
   581 L      1.000**       3.500 +- 0.013
   584 N      1.000**       3.500 +- 0.000
   614 S      1.000**       3.500 +- 0.013
   661 L      1.000**       3.500 +- 0.010
   663 T      0.999**       3.498 +- 0.067
   686 G      1.000**       3.500 +- 0.024
   690 N      0.681         2.703 +- 1.165
   696 V      0.838         3.094 +- 0.922
   728 I      1.000**       3.500 +- 0.002
   751 L      0.714         2.785 +- 1.130
   772 V      1.000**       3.499 +- 0.041
   773 F      1.000**       3.500 +- 0.009
   779 L      0.537         2.341 +- 1.247


Model 8 vs 7	1164.9842440000066

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.04.USPI71101EI7y04051pcWG2B9.JN024210_)

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

    51 A      0.773         2.616
    74 K      1.000**       3.103
   123 L      1.000**       3.103
   124 E      1.000**       3.103
   125 N      1.000**       3.103
   126 T      1.000**       3.103
   127 T      1.000**       3.103
   128 N      1.000**       3.103
   129 A      1.000**       3.103
   130 A      1.000**       3.103
   139 V      0.997**       3.098
   146 M      0.994**       3.091
   147 K      0.713         2.482
   150 Y      0.994**       3.092
   162 E      1.000**       3.103
   163 D      1.000**       3.103
   164 D      1.000**       3.103
   174 I      0.962*        3.021
   183 T      0.999**       3.101
   214 R      0.807         2.689
   251 K      0.979*        3.059
   253 T      1.000**       3.103
   265 V      0.989*        3.079
   272 N      1.000**       3.103
   280 H      0.994**       3.091
   289 E      1.000**       3.103
   296 Q      0.735         2.529
   305 K      1.000**       3.103
   308 E      0.970*        3.040
   309 K      1.000**       3.103
   311 V      1.000**       3.103
   312 E      1.000**       3.103
   315 R      0.998**       3.098
   322 T      1.000**       3.103
   324 K      0.997**       3.098
   325 P      0.989*        3.081
   326 S      1.000**       3.103
   351 Q      1.000**       3.103
   355 S      0.996**       3.096
   357 D      1.000**       3.103
   358 T      0.876         2.837
   385 R      1.000**       3.103
   387 Q      1.000**       3.103
   391 S      0.785         2.640
   405 V      1.000**       3.103
   406 N      1.000**       3.103
   407 T      1.000**       3.103
   408 T      1.000**       3.103
   443 K      1.000**       3.103
   459 V      0.897         2.882
   548 A      1.000**       3.103
   553 A      1.000**       3.103
   560 Q      1.000**       3.103
   561 K      1.000**       3.103
   562 Y      1.000**       3.103
   580 D      1.000**       3.103
   581 L      1.000**       3.103
   584 N      1.000**       3.103
   614 S      1.000**       3.103
   661 L      1.000**       3.103
   663 T      0.999**       3.102
   686 G      1.000**       3.103
   690 N      0.669         2.390
   696 V      0.869         2.820
   728 I      1.000**       3.103
   751 L      0.749         2.561
   772 V      1.000**       3.103
   773 F      1.000**       3.103
   779 L      0.556         2.140

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.04.USPI71101EI7y04051pcWG2B9.JN024210_)

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

    74 K      1.000**       3.499 +- 0.032
   123 L      1.000**       3.499 +- 0.032
   124 E      1.000**       3.499 +- 0.032
   125 N      1.000**       3.499 +- 0.032
   126 T      1.000**       3.499 +- 0.032
   127 T      1.000**       3.499 +- 0.032
   128 N      1.000**       3.499 +- 0.032
   129 A      1.000**       3.499 +- 0.032
   130 A      1.000**       3.499 +- 0.032
   139 V      0.987*        3.466 +- 0.288
   146 M      0.974*        3.433 +- 0.406
   150 Y      0.977*        3.441 +- 0.382
   162 E      1.000**       3.499 +- 0.033
   163 D      1.000**       3.499 +- 0.032
   164 D      1.000**       3.498 +- 0.048
   174 I      0.860         3.140 +- 0.892
   183 T      0.997**       3.491 +- 0.150
   251 K      0.899         3.239 +- 0.774
   253 T      1.000**       3.499 +- 0.034
   265 V      0.936         3.334 +- 0.629
   272 N      1.000**       3.499 +- 0.032
   280 H      0.974*        3.433 +- 0.406
   289 E      1.000**       3.499 +- 0.032
   305 K      0.998**       3.495 +- 0.105
   308 E      0.852         3.119 +- 0.911
   309 K      1.000**       3.499 +- 0.032
   311 V      1.000**       3.499 +- 0.037
   312 E      1.000**       3.499 +- 0.035
   315 R      0.989*        3.471 +- 0.269
   322 T      1.000**       3.499 +- 0.032
   324 K      0.989*        3.471 +- 0.269
   325 P      0.949         3.367 +- 0.567
   326 S      1.000**       3.499 +- 0.035
   351 Q      1.000**       3.499 +- 0.032
   355 S      0.982*        3.454 +- 0.338
   357 D      1.000**       3.499 +- 0.032
   358 T      0.549         2.341 +- 1.278
   385 R      0.999**       3.497 +- 0.070
   387 Q      1.000**       3.499 +- 0.032
   405 V      1.000**       3.499 +- 0.032
   406 N      1.000**       3.499 +- 0.032
   407 T      1.000**       3.499 +- 0.033
   408 T      1.000**       3.499 +- 0.032
   443 K      1.000**       3.499 +- 0.032
   459 V      0.616         2.512 +- 1.251
   548 A      1.000**       3.499 +- 0.039
   553 A      1.000**       3.499 +- 0.046
   560 Q      1.000**       3.499 +- 0.032
   561 K      1.000**       3.499 +- 0.032
   562 Y      1.000**       3.499 +- 0.046
   580 D      1.000**       3.499 +- 0.032
   581 L      1.000**       3.499 +- 0.042
   584 N      1.000**       3.499 +- 0.032
   614 S      1.000**       3.499 +- 0.042
   661 L      1.000**       3.499 +- 0.036
   663 T      0.997**       3.492 +- 0.133
   686 G      1.000**       3.498 +- 0.063
   696 V      0.575         2.403 +- 1.274
   728 I      1.000**       3.499 +- 0.033
   772 V      0.999**       3.496 +- 0.096
   773 F      1.000**       3.499 +- 0.036