--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Mar 18 10:16:48 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/GAG_1_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_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_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -17747.97        -17798.50
2     -17751.04        -17799.62
--------------------------------------
TOTAL   -17748.62        -17799.21
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_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_A1/GAG_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}         3.738079    0.018388    3.479724    4.012158    3.737135    888.42   1045.81    1.003
r(A<->C){all}   0.089414    0.000031    0.078181    0.099606    0.089356    669.68    683.54    1.009
r(A<->G){all}   0.287495    0.000221    0.258821    0.316194    0.287047    453.38    476.43    1.004
r(A<->T){all}   0.047975    0.000019    0.039622    0.056101    0.047870    771.16    797.17    1.004
r(C<->G){all}   0.045823    0.000027    0.035820    0.055943    0.045774    706.61    738.61    1.006
r(C<->T){all}   0.469394    0.000317    0.436139    0.505615    0.469824    397.23    440.44    1.010
r(G<->T){all}   0.059898    0.000038    0.047500    0.071745    0.059791    563.99    606.61    1.062
pi(A){all}      0.401985    0.000090    0.384236    0.421298    0.401816    486.78    628.14    1.002
pi(C){all}      0.199067    0.000060    0.183174    0.213420    0.199110    493.84    601.82    1.048
pi(G){all}      0.220966    0.000057    0.205744    0.234911    0.220934    633.51    647.89    1.006
pi(T){all}      0.177982    0.000060    0.163154    0.193371    0.177810    635.65    676.37    1.041
alpha{1,2}      0.340883    0.000561    0.291903    0.384577    0.339862   1113.27   1180.76    1.002
alpha{3}        2.151079    0.074632    1.644252    2.690945    2.131353   1344.51   1345.19    1.002
pinvar{all}     0.205728    0.000535    0.160916    0.250257    0.205579   1025.00   1149.94    1.003
------------------------------------------------------------------------------------------------------
* 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	-16266.313708
Model 2: PositiveSelection	-16178.783957
Model 0: one-ratio	-17191.380326
Model 3: discrete	-16121.113931
Model 7: beta	-16191.48603
Model 8: beta&w>1	-16101.849381


Model 0 vs 1	1850.1332359999979

Model 2 vs 1	175.05950200000007

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: CD.NP.11.11NP079.KU341727_)

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

    13 K      0.990**       2.788
    26 H      0.999**       2.803
    52 S      0.974*        2.759
    65 A      0.997**       2.800
    77 H      0.985*        2.779
    88 A      0.989*        2.786
    89 G      1.000**       2.806
    91 E      0.733         2.324
   113 K      0.785         2.418
   114 G      0.778         2.406
   126 L      0.700         2.264
   134 A      0.988*        2.784
   202 L      0.955*        2.726
   210 I      1.000**       2.806
   239 G      0.998**       2.803
   267 V      1.000**       2.806
   344 G      0.712         2.286
   359 S      1.000**       2.806
   360 T      0.999**       2.805
   371 S      0.994**       2.796
   424 N      0.894         2.615
   450 P      1.000**       2.806
   457 T      1.000**       2.806

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: CD.NP.11.11NP079.KU341727_)

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

    13 K      0.987*        2.550 +- 0.312
    26 H      0.998**       2.570 +- 0.271
    52 S      0.966*        2.515 +- 0.379
    65 A      0.995**       2.565 +- 0.285
    77 H      0.976*        2.536 +- 0.351
    82 T      0.510         1.774 +- 0.766
    88 A      0.985*        2.547 +- 0.318
    89 G      1.000**       2.573 +- 0.261
    91 E      0.742         2.130 +- 0.678
   113 K      0.792         2.207 +- 0.633
   114 G      0.778         2.187 +- 0.650
   126 L      0.676         2.041 +- 0.738
   134 A      0.980*        2.543 +- 0.338
   202 L      0.938         2.473 +- 0.451
   210 I      1.000**       2.573 +- 0.263
   239 G      0.998**       2.570 +- 0.272
   267 V      0.999**       2.573 +- 0.264
   344 G      0.706         2.079 +- 0.711
   359 S      1.000**       2.573 +- 0.262
   360 T      0.999**       2.572 +- 0.266
   366 S      0.515         1.780 +- 0.762
   371 S      0.991**       2.559 +- 0.300
   424 N      0.871         2.355 +- 0.563
   450 P      1.000**       2.573 +- 0.261
   457 T      1.000**       2.573 +- 0.261


Model 8 vs 7	179.27329800000007

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: CD.NP.11.11NP079.KU341727_)

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

    13 K      0.999**       2.235
    18 R      0.507         1.519
    26 H      1.000**       2.237
    52 S      0.995**       2.231
    65 A      0.999**       2.236
    77 H      0.996**       2.232
    82 T      0.831         1.993
    88 A      0.998**       2.234
    89 G      1.000**       2.237
    91 E      0.945         2.158
   113 K      0.961*        2.182
   114 G      0.955*        2.173
   126 L      0.896         2.088
   134 A      0.997**       2.233
   202 L      0.988*        2.220
   210 I      1.000**       2.237
   239 G      1.000**       2.237
   267 V      1.000**       2.237
   344 G      0.927         2.132
   359 S      1.000**       2.237
   360 T      1.000**       2.237
   366 S      0.835         2.000
   371 S      0.998**       2.235
   424 N      0.972*        2.197
   450 P      1.000**       2.237
   457 T      1.000**       2.237
   468 L      0.589         1.633

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: CD.NP.11.11NP079.KU341727_)

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

    13 K      0.986*        2.478 +- 0.184
    26 H      0.998**       2.497 +- 0.073
    52 S      0.975*        2.461 +- 0.246
    65 A      0.997**       2.496 +- 0.079
    77 H      0.987*        2.480 +- 0.178
    82 T      0.563         1.803 +- 0.793
    88 A      0.984*        2.475 +- 0.197
    89 G      1.000**       2.500 +- 0.003
    91 E      0.728         2.071 +- 0.702
   113 K      0.757         2.118 +- 0.675
   114 G      0.772         2.141 +- 0.662
   126 L      0.720         2.053 +- 0.717
   134 A      0.991**       2.485 +- 0.152
   202 L      0.959*        2.435 +- 0.313
   210 I      1.000**       2.500 +- 0.021
   239 G      0.998**       2.497 +- 0.069
   267 V      1.000**       2.500 +- 0.025
   344 G      0.737         2.083 +- 0.699
   359 S      1.000**       2.500 +- 0.025
   360 T      0.999**       2.499 +- 0.043
   366 S      0.534         1.759 +- 0.795
   371 S      0.993**       2.490 +- 0.128
   424 N      0.889         2.325 +- 0.497
   450 P      1.000**       2.500 +- 0.001
   457 T      1.000**       2.500 +- 0.007