--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Jan 29 01:35:13 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/GAG_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_5/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/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18147.53        -18191.23
2     -18146.35        -18187.48
--------------------------------------
TOTAL   -18146.77        -18190.56
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_5/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/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         3.942245    0.022384    3.638059    4.215739    3.941111   1174.10   1203.70    1.000
r(A<->C){all}   0.093571    0.000033    0.082862    0.105052    0.093451    748.07    814.42    1.001
r(A<->G){all}   0.305785    0.000248    0.275658    0.335667    0.305067    330.01    390.89    1.000
r(A<->T){all}   0.044033    0.000017    0.036390    0.052297    0.043863    777.36    873.05    1.000
r(C<->G){all}   0.053617    0.000034    0.041690    0.064154    0.053446    584.54    742.40    1.000
r(C<->T){all}   0.438156    0.000331    0.402588    0.473088    0.438596    364.16    381.95    1.001
r(G<->T){all}   0.064839    0.000038    0.052780    0.076279    0.064797    633.02    666.12    1.000
pi(A){all}      0.409437    0.000096    0.390644    0.427482    0.409388    572.64    750.49    1.000
pi(C){all}      0.191345    0.000063    0.176274    0.207003    0.191176    360.07    466.65    1.000
pi(G){all}      0.220480    0.000060    0.203430    0.234282    0.220425    654.99    676.14    1.000
pi(T){all}      0.178738    0.000059    0.163937    0.193772    0.178506    704.31    850.88    1.000
alpha{1,2}      0.358746    0.000556    0.315129    0.405625    0.357497    779.45    893.38    1.000
alpha{3}        2.558066    0.096526    1.984325    3.203797    2.530884   1341.55   1376.30    1.000
pinvar{all}     0.219938    0.000431    0.181973    0.260970    0.219380    951.50   1017.18    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	-16196.051609
Model 2: PositiveSelection	-16129.359473
Model 0: one-ratio	-17050.379215
Model 3: discrete	-16066.359146
Model 7: beta	-16105.451344
Model 8: beta&w>1	-16041.37071


Model 0 vs 1	1708.6552120000015

Model 2 vs 1	133.38427199999933

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: BC.CN.09.1471.KP234768_)

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

    26 K      0.979*        3.142
    77 F      0.997**       3.184
    89 G      0.707         2.548
   117 A      0.580         2.270
   138 P      1.000**       3.189
   207 L      1.000**       3.189
   215 N      0.749         2.639
   244 S      1.000**       3.189
   272 T      0.999**       3.188
   363 G      1.000**       3.189
   364 A      0.999**       3.187
   454 T      0.998**       3.186

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: BC.CN.09.1471.KP234768_)

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

    26 K      0.978*        3.351 +- 0.458
    77 F      0.998**       3.399 +- 0.318
    89 G      0.652         2.545 +- 1.160
   117 A      0.517         2.211 +- 1.200
   138 P      1.000**       3.404 +- 0.298
   207 L      1.000**       3.403 +- 0.300
   215 N      0.714         2.699 +- 1.110
   244 S      1.000**       3.404 +- 0.298
   272 T      0.999**       3.403 +- 0.303
   363 G      1.000**       3.404 +- 0.298
   364 A      0.999**       3.401 +- 0.308
   454 T      0.999**       3.401 +- 0.311


Model 8 vs 7	128.16126799999984

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: BC.CN.09.1471.KP234768_)

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

    26 K      0.984*        2.576
    77 F      0.998**       2.599
    89 G      0.851         2.352
   117 A      0.783         2.236
   138 P      1.000**       2.602
   207 L      1.000**       2.602
   215 N      0.875         2.392
   244 S      1.000**       2.602
   272 T      0.999**       2.602
   363 G      1.000**       2.602
   364 A      0.999**       2.601
   370 S      0.605         1.932
   454 T      0.999**       2.600

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: BC.CN.09.1471.KP234768_)

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

    26 K      0.987*        2.484 +- 0.186
    77 F      0.998**       2.501 +- 0.094
    82 T      0.588         1.850 +- 0.780
    89 G      0.892         2.332 +- 0.489
   117 A      0.843         2.255 +- 0.572
   138 P      1.000**       2.504 +- 0.065
   207 L      1.000**       2.504 +- 0.069
   215 N      0.908         2.358 +- 0.457
   244 S      1.000**       2.504 +- 0.065
   272 T      0.999**       2.503 +- 0.074
   363 G      1.000**       2.504 +- 0.065
   364 A      0.999**       2.503 +- 0.077
   370 S      0.707         2.039 +- 0.719
   454 T      0.999**       2.503 +- 0.083