--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 18 17:30:30 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-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -15096.74        -15111.64
2     -15095.61        -15112.36
--------------------------------------
TOTAL   -15096.03        -15112.06
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.349686    0.002688    1.251258    1.452087    1.348476   1395.45   1448.23    1.001
r(A<->C){all}   0.101127    0.000084    0.083596    0.119610    0.100825    888.01    988.98    1.002
r(A<->G){all}   0.216299    0.000174    0.190926    0.242217    0.215987    996.42   1021.34    1.000
r(A<->T){all}   0.122610    0.000154    0.100925    0.148442    0.122445    999.64   1029.37    1.001
r(C<->G){all}   0.042169    0.000024    0.033055    0.051616    0.041961    860.43   1024.55    1.000
r(C<->T){all}   0.454089    0.000312    0.418655    0.487784    0.454149    934.56    944.51    1.001
r(G<->T){all}   0.063706    0.000048    0.050133    0.077389    0.063396   1041.40   1117.29    1.000
pi(A){all}      0.215468    0.000034    0.204509    0.226715    0.215424    930.65   1002.12    1.000
pi(C){all}      0.284435    0.000038    0.272841    0.296385    0.284336    880.48    937.04    1.000
pi(G){all}      0.310504    0.000045    0.297046    0.323221    0.310322    835.69    865.60    1.000
pi(T){all}      0.189594    0.000029    0.178657    0.199653    0.189523    842.08    911.02    1.000
alpha{1,2}      0.124026    0.000037    0.112893    0.136609    0.123853   1126.84   1201.48    1.000
alpha{3}        6.466085    1.465477    4.263936    8.901446    6.353301   1258.08   1379.54    1.000
pinvar{all}     0.271561    0.000409    0.231396    0.311446    0.271754   1173.05   1237.87    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	-13495.123426
Model 0: one-ratio	-13634.385871
Model 3: discrete	-13474.623958
Model 7: beta	-13477.695254
Model 8: beta&w>1	-13472.789692


Model 0 vs 1	278.52492800000255

Model 2 vs 1	3.80000019504223E-5

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-PB)

            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-PB)

            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