--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 18 19:24:10 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/285/Kdm2-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/285/Kdm2-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-PD/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/285/Kdm2-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -15095.99        -15112.04
2     -15094.56        -15110.28
--------------------------------------
TOTAL   -15095.04        -15111.51
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/285/Kdm2-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/285/Kdm2-PD/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/285/Kdm2-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.351284    0.002591    1.246232    1.444481    1.349867   1288.46   1331.95    1.000
r(A<->C){all}   0.101091    0.000076    0.083707    0.118178    0.100781    921.02    959.68    1.002
r(A<->G){all}   0.216416    0.000172    0.190035    0.240708    0.216230   1017.00   1051.59    1.001
r(A<->T){all}   0.122294    0.000143    0.099211    0.146100    0.121916    789.45    908.58    1.000
r(C<->G){all}   0.042290    0.000022    0.033145    0.051209    0.042251    781.25    849.16    1.001
r(C<->T){all}   0.454281    0.000302    0.420273    0.487348    0.454762    836.98    851.57    1.001
r(G<->T){all}   0.063628    0.000048    0.050560    0.076817    0.063501    938.22   1030.21    1.001
pi(A){all}      0.215438    0.000035    0.204335    0.227356    0.215524   1075.86   1083.03    1.000
pi(C){all}      0.284444    0.000039    0.271794    0.296122    0.284225   1072.36   1140.65    1.000
pi(G){all}      0.310585    0.000044    0.296374    0.322889    0.310326    968.75   1006.04    1.000
pi(T){all}      0.189533    0.000030    0.179329    0.199939    0.189600    864.37    997.57    1.000
alpha{1,2}      0.123770    0.000038    0.112770    0.136350    0.123675   1379.43   1380.63    1.000
alpha{3}        6.475202    1.457845    4.280081    8.900411    6.320313   1338.77   1380.45    1.001
pinvar{all}     0.271481    0.000402    0.230381    0.308071    0.271691   1014.89   1085.30    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	-13495.123407
Model 2: PositiveSelection	-13495.123407
Model 0: one-ratio	-13634.385871
Model 3: discrete	-13472.075762
Model 7: beta	-13477.695254
Model 8: beta&w>1	-13472.789692


Model 0 vs 1	278.52492800000255

Model 2 vs 1	0.0

Model 8 vs 7	9.811123999999836

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Kdm2-PD)

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

   581 S      0.536         0.833
   583 G      0.988*        1.299
   816 A      0.878         1.185
   823 N      0.582         0.881
   929 V      0.866         1.173
  1032 S      0.933         1.242

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: D_melanogaster_Kdm2-PD)

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

   581 S      0.751         1.265 +- 0.420
   583 G      0.975*        1.480 +- 0.126
   586 P      0.737         1.243 +- 0.445
   592 A      0.581         1.080 +- 0.514
   600 G      0.688         1.206 +- 0.451
   605 P      0.598         1.093 +- 0.516
   816 A      0.871         1.390 +- 0.293
   823 N      0.753         1.271 +- 0.412
   929 V      0.891         1.406 +- 0.276
  1032 S      0.937         1.448 +- 0.208