--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 09:14:12 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-PE/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -20283.09        -20302.54
2     -20282.28        -20299.68
--------------------------------------
TOTAL   -20282.61        -20301.90
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.918695    0.001058    0.856738    0.984775    0.917496   1301.44   1401.22    1.000
r(A<->C){all}   0.086333    0.000053    0.071684    0.099756    0.086274   1017.00   1091.69    1.001
r(A<->G){all}   0.255225    0.000180    0.229172    0.280425    0.254574    887.77    979.47    1.000
r(A<->T){all}   0.117052    0.000129    0.095152    0.139590    0.116817    952.74    969.98    1.001
r(C<->G){all}   0.078333    0.000030    0.067582    0.088766    0.078224    811.49    984.71    1.000
r(C<->T){all}   0.399717    0.000241    0.370292    0.430548    0.399597    879.59    906.62    1.000
r(G<->T){all}   0.063339    0.000043    0.050668    0.076041    0.063193   1084.10   1084.37    1.000
pi(A){all}      0.213610    0.000023    0.204357    0.223300    0.213434    932.02    964.60    1.001
pi(C){all}      0.308968    0.000029    0.298072    0.319243    0.309119    701.05    840.44    1.000
pi(G){all}      0.292811    0.000030    0.282565    0.303892    0.292788    673.06    772.86    1.000
pi(T){all}      0.184612    0.000021    0.175470    0.193048    0.184629    823.38    892.80    1.000
alpha{1,2}      0.125092    0.000036    0.113567    0.136542    0.124805   1358.61   1429.81    1.000
alpha{3}        5.516332    1.012104    3.582335    7.442331    5.420477   1375.83   1438.42    1.000
pinvar{all}     0.477290    0.000227    0.448434    0.506941    0.477502   1292.05   1366.76    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	-18363.248021
Model 2: PositiveSelection	-18363.248021
Model 0: one-ratio	-18553.060887
Model 3: discrete	-18346.438263
Model 7: beta	-18368.185201
Model 8: beta&w>1	-18350.581288


Model 0 vs 1	379.6257320000004

Model 2 vs 1	0.0

Model 8 vs 7	35.20782599999802

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-PE)

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

    48 S      0.601         0.897
    55 C      0.995**       1.359
    56 S      1.000**       1.365
    62 V      0.940         1.295
    63 S      0.779         1.106
   134 T      0.974*        1.334
   948 Q      0.610         0.908
  1350 G      0.795         1.124
  1351 P      0.853         1.193
  1362 V      0.525         0.809
  1565 I      0.985*        1.347
  1566 A      0.592         0.886
  1570 A      0.996**       1.360

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-PE)

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

    48 S      0.629         1.128 +- 0.504
    55 C      0.963*        1.471 +- 0.163
    56 S      0.991**       1.495 +- 0.080
    62 V      0.814         1.336 +- 0.355
    63 S      0.682         1.201 +- 0.453
   134 T      0.927         1.438 +- 0.233
   948 Q      0.539         1.053 +- 0.503
  1350 G      0.786         1.295 +- 0.410
  1351 P      0.775         1.292 +- 0.400
  1362 V      0.578         1.070 +- 0.525
  1563 A      0.551         1.041 +- 0.531
  1565 I      0.922         1.435 +- 0.236
  1566 A      0.529         1.041 +- 0.506
  1570 A      0.968*        1.475 +- 0.151