--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Feb 10 03:36:34 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -29294.16        -29335.91
2     -29290.05        -29330.12
--------------------------------------
TOTAL   -29290.73        -29335.22
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_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}         3.025380    0.007731    2.849271    3.191844    3.024690   1211.82   1315.97    1.000
r(A<->C){all}   0.077046    0.000016    0.069749    0.084951    0.077051    698.39    706.38    1.000
r(A<->G){all}   0.372788    0.000185    0.345021    0.398314    0.372560    332.90    383.68    1.002
r(A<->T){all}   0.038019    0.000007    0.033240    0.043029    0.037954    664.41    704.96    1.000
r(C<->G){all}   0.029808    0.000013    0.023045    0.037032    0.029563    805.87    871.35    1.000
r(C<->T){all}   0.443925    0.000205    0.414947    0.469977    0.444149    327.31    362.21    1.002
r(G<->T){all}   0.038414    0.000012    0.031867    0.045197    0.038370    799.50    808.66    1.002
pi(A){all}      0.405195    0.000052    0.390890    0.418645    0.405402    671.93    683.87    1.000
pi(C){all}      0.178187    0.000031    0.167600    0.189189    0.178153    582.61    582.62    1.000
pi(G){all}      0.206618    0.000035    0.194570    0.218007    0.206711    592.97    691.75    1.002
pi(T){all}      0.210000    0.000037    0.198688    0.222128    0.210029    556.26    583.72    1.001
alpha{1,2}      0.267008    0.000223    0.238769    0.296443    0.266618   1155.38   1297.75    1.000
alpha{3}        2.327650    0.066804    1.810664    2.801887    2.316513    975.66   1202.89    1.002
pinvar{all}     0.265641    0.000352    0.230841    0.303320    0.265794   1030.77   1154.94    1.001
------------------------------------------------------------------------------------------------------
* 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	-28722.613283
Model 2: PositiveSelection	-28636.150282
Model 0: one-ratio	-30080.551681
Model 3: discrete	-28515.40265
Model 7: beta	-28566.048946
Model 8: beta&w>1	-28460.402236


Model 0 vs 1	2715.876796000004

Model 2 vs 1	172.92600200000015

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.TH.05.AA029b10L.JX447033_)

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

    16 S      0.980*        3.311
    30 G      0.998**       3.354
    42 F      0.899         3.120
    44 F      0.669         2.578
   107 L      1.000**       3.359
   266 S      1.000**       3.359
   350 A      0.943         3.225
   354 S      0.999**       3.357
   388 E      1.000**       3.359
   429 A      0.988*        3.331
   477 Q      1.000**       3.358
   519 A      0.996**       3.349
   595 L      0.958*        3.259
   611 S      0.992**       3.340
   626 H      1.000**       3.358
   697 S      1.000**       3.359
   720 S      0.504         2.189

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: 01_AE.TH.05.AA029b10L.JX447033_)

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

    16 S      0.990*        3.454 +- 0.286
    30 G      0.999**       3.477 +- 0.164
    41 S      0.549         2.359 +- 1.237
    42 F      0.942         3.334 +- 0.598
    44 F      0.790         2.957 +- 1.018
   107 L      1.000**       3.479 +- 0.144
   266 S      1.000**       3.479 +- 0.145
   350 A      0.967*        3.398 +- 0.463
   354 S      1.000**       3.478 +- 0.151
   388 E      1.000**       3.479 +- 0.144
   429 A      0.994**       3.464 +- 0.238
   477 Q      1.000**       3.479 +- 0.148
   519 A      0.998**       3.474 +- 0.184
   595 L      0.977*        3.421 +- 0.401
   611 S      0.996**       3.470 +- 0.210
   626 H      1.000**       3.478 +- 0.149
   697 S      1.000**       3.479 +- 0.144
   720 S      0.607         2.499 +- 1.213
   804 L      0.595         2.473 +- 1.221


Model 8 vs 7	211.2934199999945

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.TH.05.AA029b10L.JX447033_)

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

    11 K      0.863         2.215
    16 S      0.998**       2.447
    21 A      0.822         2.143
    30 G      1.000**       2.450
    41 S      0.834         2.161
    42 F      0.993**       2.438
    44 F      0.949         2.361
   107 L      1.000**       2.450
   266 S      1.000**       2.450
   278 I      0.874         2.233
   305 C      0.657         1.859
   350 A      0.998**       2.446
   354 S      1.000**       2.450
   358 T      0.802         2.107
   388 E      1.000**       2.450
   429 A      0.999**       2.449
   477 Q      1.000**       2.450
   519 A      1.000**       2.450
   595 L      0.998**       2.446
   611 S      0.999**       2.449
   626 H      1.000**       2.450
   634 S      0.941         2.349
   697 S      1.000**       2.450
   720 S      0.978*        2.412
   775 V      0.916         2.305
   804 L      0.870         2.225
   827 A      0.777         2.066

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: 01_AE.TH.05.AA029b10L.JX447033_)

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

    11 K      0.793         2.169 +- 0.650
    16 S      0.996**       2.494 +- 0.098
    21 A      0.815         2.200 +- 0.633
    30 G      0.999**       2.499 +- 0.040
    41 S      0.850         2.254 +- 0.587
    42 F      0.986*        2.478 +- 0.186
    44 F      0.941         2.405 +- 0.381
   107 L      1.000**       2.500 +- 0.004
   266 S      1.000**       2.500 +- 0.011
   278 I      0.677         1.989 +- 0.741
   305 C      0.552         1.780 +- 0.800
   350 A      0.992**       2.487 +- 0.143
   354 S      1.000**       2.500 +- 0.020
   358 T      0.782         2.147 +- 0.671
   388 E      1.000**       2.500 +- 0.004
   429 A      0.998**       2.497 +- 0.071
   477 Q      1.000**       2.500 +- 0.018
   519 A      0.999**       2.499 +- 0.047
   595 L      0.994**       2.490 +- 0.127
   611 S      0.998**       2.497 +- 0.069
   626 H      1.000**       2.500 +- 0.019
   634 S      0.899         2.338 +- 0.483
   697 S      1.000**       2.500 +- 0.005
   720 S      0.948         2.418 +- 0.352
   775 V      0.864         2.283 +- 0.548
   804 L      0.860         2.273 +- 0.564
   827 A      0.688         2.000 +- 0.744