--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Feb 12 06:04:32 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_N2/POL_1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -32200.00        -32240.54
2     -32197.19        -32237.04
--------------------------------------
TOTAL   -32197.82        -32239.88
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_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}         4.528076    0.022500    4.238315    4.825170    4.521645    514.52    782.28    1.000
r(A<->C){all}   0.080871    0.000015    0.073167    0.088600    0.080777    794.03    809.91    1.000
r(A<->G){all}   0.346356    0.000178    0.317368    0.371422    0.346772    289.45    307.69    1.000
r(A<->T){all}   0.034837    0.000006    0.030259    0.039725    0.034722    616.54    680.57    1.000
r(C<->G){all}   0.036741    0.000016    0.029067    0.044800    0.036634    511.65    592.14    1.001
r(C<->T){all}   0.464710    0.000202    0.435600    0.491353    0.464635    255.63    275.82    1.000
r(G<->T){all}   0.036485    0.000011    0.030119    0.042840    0.036431    824.78    828.67    1.000
pi(A){all}      0.419994    0.000049    0.406275    0.433531    0.419819    440.95    517.53    1.000
pi(C){all}      0.168446    0.000028    0.157954    0.178537    0.168374    446.19    449.13    1.000
pi(G){all}      0.204878    0.000028    0.194317    0.214761    0.204916    498.39    563.89    1.000
pi(T){all}      0.206683    0.000034    0.196076    0.218470    0.206542    430.76    492.63    1.000
alpha{1,2}      0.267239    0.000161    0.240936    0.290561    0.267113   1097.08   1144.55    1.000
alpha{3}        2.485673    0.051842    2.070056    2.943386    2.472733   1256.15   1288.56    1.000
pinvar{all}     0.232979    0.000262    0.201076    0.264822    0.233068    627.89    869.74    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	-31020.236433
Model 2: PositiveSelection	-30867.336546
Model 0: one-ratio	-32712.450941
Model 3: discrete	-30685.050346
Model 7: beta	-30804.215158
Model 8: beta&w>1	-30631.594021


Model 0 vs 1	3384.429016000002

Model 2 vs 1	305.79977399999916

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.11.AMBI_CLONE.KU641402_)

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

    17 P      1.000**       4.215
    32 T      1.000**       4.215
    33 F      0.998**       4.210
    98 S      1.000**       4.215
   344 R      0.999**       4.212
   378 V      1.000**       4.215
   419 A      0.994**       4.194
   467 Q      1.000**       4.215
   509 A      0.994**       4.196
   601 S      1.000**       4.215
   616 H      0.998**       4.210
   687 T      1.000**       4.215
   812 S      1.000**       4.215
   817 T      1.000**       4.215

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.11.AMBI_CLONE.KU641402_)

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

    17 P      1.000**       3.685 +- 0.389
    32 T      1.000**       3.685 +- 0.389
    33 F      0.999**       3.684 +- 0.393
    98 S      1.000**       3.685 +- 0.389
   256 D      0.695         2.797 +- 1.212
   344 R      1.000**       3.684 +- 0.391
   378 V      1.000**       3.685 +- 0.389
   419 A      0.998**       3.679 +- 0.408
   467 Q      1.000**       3.685 +- 0.389
   490 V      0.649         2.637 +- 1.210
   509 A      0.998**       3.679 +- 0.407
   510 T      0.721         2.827 +- 1.145
   601 S      1.000**       3.685 +- 0.389
   616 H      1.000**       3.684 +- 0.393
   624 L      0.661         2.688 +- 1.224
   687 T      1.000**       3.685 +- 0.389
   812 S      1.000**       3.685 +- 0.389
   817 T      1.000**       3.685 +- 0.389


Model 8 vs 7	345.24227399999654

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.11.AMBI_CLONE.KU641402_)

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

    17 P      1.000**       2.643
    30 Q      0.746         2.143
    32 T      1.000**       2.643
    33 F      1.000**       2.643
    35 F      0.619         1.890
    72 S      0.875         2.397
    98 S      1.000**       2.643
   256 D      0.990**       2.624
   344 R      1.000**       2.643
   378 V      1.000**       2.643
   419 A      1.000**       2.643
   467 Q      1.000**       2.643
   490 V      0.999**       2.641
   509 A      1.000**       2.643
   510 T      0.999**       2.642
   568 V      0.987*        2.618
   585 L      0.953*        2.551
   601 S      1.000**       2.643
   616 H      1.000**       2.643
   624 L      0.993**       2.629
   687 T      1.000**       2.643
   765 V      0.957*        2.558
   767 L      0.803         2.254
   812 S      1.000**       2.643
   817 T      1.000**       2.643

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.11.AMBI_CLONE.KU641402_)

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

    17 P      1.000**       2.524 +- 0.152
    21 A      0.537         1.735 +- 0.833
    30 Q      0.745         2.088 +- 0.717
    32 T      1.000**       2.524 +- 0.152
    33 F      1.000**       2.523 +- 0.153
    35 F      0.689         1.991 +- 0.774
    72 S      0.744         2.093 +- 0.697
    98 S      1.000**       2.524 +- 0.152
   256 D      0.972*        2.474 +- 0.300
   344 R      1.000**       2.524 +- 0.152
   378 V      1.000**       2.524 +- 0.152
   419 A      0.999**       2.523 +- 0.156
   467 Q      1.000**       2.524 +- 0.152
   490 V      0.980*        2.484 +- 0.252
   509 A      0.999**       2.523 +- 0.156
   510 T      0.986*        2.495 +- 0.226
   568 V      0.918         2.374 +- 0.439
   585 L      0.899         2.347 +- 0.494
   601 S      1.000**       2.524 +- 0.152
   616 H      1.000**       2.523 +- 0.153
   624 L      0.973*        2.474 +- 0.293
   687 T      1.000**       2.524 +- 0.152
   765 V      0.918         2.380 +- 0.457
   767 L      0.842         2.251 +- 0.626
   794 L      0.520         1.705 +- 0.840
   812 S      1.000**       2.524 +- 0.152
   817 T      1.000**       2.524 +- 0.152