--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Mar 19 21:09:11 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_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/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18505.51        -18545.46
2     -18502.76        -18550.25
--------------------------------------
TOTAL   -18503.40        -18549.56
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_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/GAG_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}         3.916369    0.017075    3.632718    4.149444    3.913813   1501.00   1501.00    1.001
r(A<->C){all}   0.086823    0.000029    0.076822    0.097348    0.086778    688.01    718.36    1.000
r(A<->G){all}   0.318617    0.000226    0.289993    0.348008    0.318468    285.59    406.09    1.000
r(A<->T){all}   0.050718    0.000018    0.042162    0.058523    0.050529    686.83    784.26    1.000
r(C<->G){all}   0.043157    0.000024    0.033675    0.052712    0.042958    686.75    695.18    1.000
r(C<->T){all}   0.443194    0.000282    0.410512    0.474548    0.443134    307.95    409.52    1.000
r(G<->T){all}   0.057492    0.000032    0.046489    0.068528    0.057246    778.53    839.42    1.001
pi(A){all}      0.405850    0.000089    0.388685    0.425482    0.405577    450.36    557.75    1.000
pi(C){all}      0.198091    0.000059    0.182045    0.212113    0.197985    357.13    510.46    1.000
pi(G){all}      0.222202    0.000059    0.206436    0.236589    0.222089    560.12    597.37    1.000
pi(T){all}      0.173857    0.000053    0.159562    0.187708    0.173760    646.29    696.25    1.000
alpha{1,2}      0.299064    0.000373    0.261232    0.336160    0.297900   1081.55   1182.31    1.000
alpha{3}        1.836839    0.048089    1.427314    2.271389    1.824914   1399.82   1412.65    1.000
pinvar{all}     0.153344    0.000546    0.109483    0.203360    0.153389   1075.73   1196.84    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	-16269.578845
Model 2: PositiveSelection	-16208.112831
Model 0: one-ratio	-17249.075527
Model 3: discrete	-16141.0638
Model 7: beta	-16174.633061
Model 8: beta&w>1	-16117.384529


Model 0 vs 1	1958.9933640000017

Model 2 vs 1	122.93202799999926

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: F1.BR.07.07BR844.FJ771010_)

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

    26 K      0.722         2.281
    67 Q      0.762         2.352
    73 L      0.613         2.088
    77 Y      0.998**       2.770
    82 V      0.999**       2.773
    89 K      0.989*        2.755
   129 S      1.000**       2.775
   198 L      0.998**       2.770
   235 S      0.906         2.609
   263 V      1.000**       2.774
   340 S      0.777         2.378
   355 T      0.998**       2.771
   356 A      0.999**       2.773
   419 H      0.818         2.451
   443 Q      1.000**       2.774
   447 A      0.998**       2.770
   458 E      0.980*        2.739

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: F1.BR.07.07BR844.FJ771010_)

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

    26 K      0.737         2.133 +- 0.696
    67 Q      0.753         2.166 +- 0.695
    73 L      0.598         1.926 +- 0.777
    77 Y      0.996**       2.570 +- 0.281
    82 V      0.998**       2.573 +- 0.272
    89 K      0.986*        2.554 +- 0.320
   129 S      1.000**       2.576 +- 0.264
   198 L      0.997**       2.570 +- 0.280
   206 I      0.537         1.816 +- 0.765
   235 S      0.900         2.398 +- 0.514
   263 V      1.000**       2.575 +- 0.266
   340 S      0.775         2.196 +- 0.667
   354 N      0.510         1.772 +- 0.763
   355 T      0.997**       2.571 +- 0.276
   356 A      0.999**       2.574 +- 0.270
   419 H      0.810         2.256 +- 0.638
   443 Q      1.000**       2.575 +- 0.265
   447 A      0.997**       2.570 +- 0.280
   458 E      0.972*        2.532 +- 0.369


Model 8 vs 7	114.49706399999923

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: F1.BR.07.07BR844.FJ771010_)

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

    26 K      0.856         2.002
    67 Q      0.874         2.024
    73 L      0.768         1.884
    77 Y      0.998**       2.184
    82 V      0.999**       2.185
    89 K      0.992**       2.176
   129 S      1.000**       2.186
   198 L      0.998**       2.184
   206 I      0.747         1.861
   235 S      0.956*        2.131
   263 V      1.000**       2.186
   286 T      0.520         1.565
   340 S      0.902         2.061
   353 T      0.516         1.566
   354 N      0.705         1.807
   355 T      0.999**       2.184
   356 A      0.999**       2.185
   419 H      0.904         2.064
   443 Q      1.000**       2.186
   447 A      0.998**       2.184
   458 E      0.986*        2.169

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: F1.BR.07.07BR844.FJ771010_)

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

    26 K      0.771         2.140 +- 0.661
    67 Q      0.836         2.240 +- 0.587
    73 L      0.734         2.074 +- 0.710
    77 Y      0.999**       2.498 +- 0.059
    82 V      0.999**       2.499 +- 0.040
    89 K      0.992**       2.487 +- 0.144
   129 S      1.000**       2.500 +- 0.004
   198 L      0.998**       2.497 +- 0.066
   206 I      0.627         1.908 +- 0.768
   235 S      0.929         2.388 +- 0.404
   263 V      1.000**       2.500 +- 0.015
   340 S      0.858         2.275 +- 0.552
   354 N      0.545         1.780 +- 0.789
   355 T      0.998**       2.497 +- 0.066
   356 A      0.999**       2.499 +- 0.040
   419 H      0.865         2.287 +- 0.540
   443 Q      1.000**       2.500 +- 0.010
   447 A      0.999**       2.498 +- 0.060
   458 E      0.990*        2.483 +- 0.161