--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 16:29:26 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/423/Trpm-PJ/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/423/Trpm-PJ/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/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -16483.41        -16501.67
2     -16483.88        -16500.54
--------------------------------------
TOTAL   -16483.62        -16501.25
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/423/Trpm-PJ/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/423/Trpm-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.776225    0.001003    0.715548    0.838193    0.775973   1363.44   1432.22    1.001
r(A<->C){all}   0.084552    0.000068    0.069403    0.102197    0.084182   1168.68   1198.64    1.000
r(A<->G){all}   0.251603    0.000225    0.221670    0.280823    0.250993   1046.91   1079.77    1.000
r(A<->T){all}   0.110640    0.000164    0.086811    0.137402    0.110162    943.23    955.62    1.000
r(C<->G){all}   0.068055    0.000032    0.057814    0.079730    0.067865   1222.58   1258.69    1.000
r(C<->T){all}   0.426703    0.000326    0.392479    0.462222    0.426597    909.63    934.46    1.000
r(G<->T){all}   0.058448    0.000053    0.045274    0.073090    0.058232   1048.61   1140.32    1.000
pi(A){all}      0.214371    0.000029    0.203774    0.224580    0.214217   1150.07   1162.48    1.000
pi(C){all}      0.307492    0.000035    0.296584    0.319954    0.307543    976.58   1045.00    1.000
pi(G){all}      0.294482    0.000034    0.283248    0.305861    0.294467    836.50    940.96    1.000
pi(T){all}      0.183655    0.000024    0.173597    0.192283    0.183778    894.61   1044.80    1.000
alpha{1,2}      0.111514    0.000039    0.099867    0.123860    0.111289   1436.48   1467.15    1.000
alpha{3}        6.391538    1.423226    4.307163    8.832141    6.272657   1501.00   1501.00    1.000
pinvar{all}     0.505290    0.000254    0.474148    0.536118    0.505433   1209.31   1230.63    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	-15046.189274
Model 2: PositiveSelection	-15046.189274
Model 0: one-ratio	-15129.554409
Model 3: discrete	-15035.537163
Model 7: beta	-15039.068796
Model 8: beta&w>1	-15031.160836


Model 0 vs 1	166.73027000000002

Model 2 vs 1	0.0

Model 8 vs 7	15.815920000000915

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_Trpm-PJ)

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

    36 T      0.862         2.048
  1233 G      0.800         1.915
  1248 V      0.504         1.275
  1451 I      0.993**       2.333
  1456 A      0.988*        2.323

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_Trpm-PJ)

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

    36 T      0.875         1.402 +- 0.358
  1233 G      0.850         1.377 +- 0.383
  1234 P      0.695         1.209 +- 0.496
  1248 V      0.740         1.259 +- 0.473
  1451 I      0.953*        1.481 +- 0.241
  1456 A      0.949         1.478 +- 0.251
  1691 T      0.518         0.968 +- 0.600
  1769 Q      0.694         1.210 +- 0.492