--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Feb 11 13:36:11 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_N2/POL_1_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -32411.62        -32455.16
2     -32412.44        -32451.69
--------------------------------------
TOTAL   -32411.95        -32454.50
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.412408    0.021471    4.145539    4.711587    4.409860    663.62    705.10    1.000
r(A<->C){all}   0.073778    0.000014    0.066835    0.080844    0.073671    646.73    682.76    1.000
r(A<->G){all}   0.346123    0.000178    0.319883    0.371248    0.346186    356.69    404.03    1.002
r(A<->T){all}   0.034767    0.000007    0.030161    0.040460    0.034644    689.19    692.07    1.000
r(C<->G){all}   0.040412    0.000016    0.032595    0.048187    0.040191    646.37    720.41    1.000
r(C<->T){all}   0.462400    0.000205    0.435443    0.491306    0.462243    352.86    393.69    1.002
r(G<->T){all}   0.042520    0.000013    0.035538    0.049704    0.042426    749.95    836.96    1.000
pi(A){all}      0.417173    0.000051    0.402278    0.430204    0.417234    429.63    474.45    1.000
pi(C){all}      0.175578    0.000027    0.164797    0.184846    0.175477    462.58    552.23    1.001
pi(G){all}      0.203208    0.000033    0.193026    0.215333    0.203088    496.46    612.03    1.000
pi(T){all}      0.204042    0.000032    0.193506    0.215355    0.204010    680.97    682.94    1.000
alpha{1,2}      0.298749    0.000226    0.268436    0.327047    0.298491    941.75   1131.59    1.000
alpha{3}        2.193268    0.043366    1.819823    2.619593    2.185551   1180.09   1224.23    1.000
pinvar{all}     0.238728    0.000304    0.203745    0.271047    0.238809    900.61    956.17    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	-31434.778169
Model 2: PositiveSelection	-31345.916802
Model 0: one-ratio	-33050.813068
Model 3: discrete	-31176.003452
Model 7: beta	-31228.681779
Model 8: beta&w>1	-31116.540357


Model 0 vs 1	3232.069798000004

Model 2 vs 1	177.72273400000267

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.BR.10.10BR_PE019.KT427740_)

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

    17 S      0.990*        3.165
    32 A      0.905         2.979
    36 L      0.999**       3.186
    37 N      0.559         2.222
   101 P      1.000**       3.188
   260 E      0.962*        3.103
   348 Q      0.961*        3.102
   382 K      1.000**       3.188
   423 T      0.673         2.472
   471 Q      1.000**       3.187
   513 S      0.891         2.949
   589 L      0.938         3.052
   605 P      0.997**       3.181
   620 H      0.988*        3.161
   691 S      1.000**       3.188
   798 I      0.938         3.051
   816 S      0.958*        3.097
   821 N      1.000**       3.188

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.BR.10.10BR_PE019.KT427740_)

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

    17 S      0.994**       3.271 +- 0.445
    32 A      0.940         3.141 +- 0.675
    35 S      0.534         2.192 +- 1.160
    36 L      0.999**       3.282 +- 0.415
    37 N      0.638         2.403 +- 1.119
   101 P      1.000**       3.283 +- 0.412
   131 L      0.515         2.131 +- 1.146
   260 E      0.975*        3.224 +- 0.541
   348 Q      0.976*        3.227 +- 0.537
   382 K      1.000**       3.283 +- 0.412
   423 T      0.766         2.722 +- 1.025
   471 Q      1.000**       3.283 +- 0.413
   513 S      0.935         3.132 +- 0.690
   589 L      0.963*        3.197 +- 0.591
   605 P      0.998**       3.280 +- 0.422
   620 H      0.993**       3.267 +- 0.453
   628 L      0.529         2.140 +- 1.130
   691 S      1.000**       3.283 +- 0.412
   798 I      0.966*        3.204 +- 0.581
   816 S      0.972*        3.217 +- 0.553
   821 N      1.000**       3.283 +- 0.412


Model 8 vs 7	224.28284399999393

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.BR.10.10BR_PE019.KT427740_)

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

     5 T      0.636         1.567
    17 S      1.000**       2.088
    18 S      0.530         1.413
    21 T      0.936         1.996
    28 R      0.759         1.743
    30 D      0.966*        2.039
    32 A      0.998**       2.086
    35 S      0.911         1.960
    36 L      1.000**       2.089
    37 N      0.994**       2.080
    38 L      0.572         1.470
    99 Q      0.501         1.368
   101 P      1.000**       2.089
   131 L      0.948         2.014
   260 E      1.000**       2.088
   348 Q      1.000**       2.088
   382 K      1.000**       2.089
   423 T      0.992**       2.077
   471 Q      1.000**       2.089
   483 F      0.888         1.928
   494 M      0.987*        2.070
   513 S      0.996**       2.083
   514 T      0.731         1.702
   523 I      0.915         1.967
   572 A      0.699         1.657
   589 L      0.999**       2.087
   605 P      1.000**       2.088
   620 H      1.000**       2.088
   628 L      0.990*        2.074
   691 S      1.000**       2.089
   769 I      0.646         1.580
   798 I      0.998**       2.086
   816 S      1.000**       2.088
   821 N      1.000**       2.089

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.BR.10.10BR_PE019.KT427740_)

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

    17 S      0.998**       2.496 +- 0.075
    21 T      0.786         2.154 +- 0.666
    30 D      0.618         1.892 +- 0.776
    32 A      0.984*        2.475 +- 0.197
    35 S      0.821         2.207 +- 0.629
    36 L      1.000**       2.500 +- 0.027
    37 N      0.917         2.368 +- 0.440
   101 P      1.000**       2.500 +- 0.001
   131 L      0.813         2.199 +- 0.631
   260 E      0.993**       2.489 +- 0.129
   348 Q      0.993**       2.489 +- 0.131
   382 K      1.000**       2.500 +- 0.001
   423 T      0.947         2.415 +- 0.359
   471 Q      1.000**       2.500 +- 0.013
   483 F      0.582         1.825 +- 0.800
   494 M      0.558         1.801 +- 0.787
   513 S      0.982*        2.471 +- 0.215
   523 I      0.549         1.775 +- 0.803
   589 L      0.986*        2.477 +- 0.188
   605 P      0.999**       2.499 +- 0.047
   620 H      0.997**       2.495 +- 0.087
   628 L      0.883         2.313 +- 0.513
   691 S      1.000**       2.500 +- 0.001
   798 I      0.986*        2.478 +- 0.184
   816 S      0.993**       2.489 +- 0.131
   821 N      1.000**       2.500 +- 0.003