--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Dec 07 15:30:01 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/408/Sudx-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/408/Sudx-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PC/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/408/Sudx-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -10162.86        -10176.96
2     -10162.32        -10179.32
--------------------------------------
TOTAL   -10162.55        -10178.72
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/408/Sudx-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PC/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/408/Sudx-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.280388    0.003679    1.163325    1.396784    1.279156   1360.70   1430.85    1.000
r(A<->C){all}   0.093585    0.000095    0.075321    0.113268    0.093235    890.67    949.23    1.000
r(A<->G){all}   0.285060    0.000328    0.248982    0.319985    0.285399    833.47    914.29    1.000
r(A<->T){all}   0.074898    0.000149    0.052286    0.099518    0.074249    743.68    944.01    1.000
r(C<->G){all}   0.036286    0.000029    0.025831    0.047051    0.036208   1035.84   1151.56    1.000
r(C<->T){all}   0.439082    0.000445    0.397286    0.479124    0.439485    888.32    908.73    1.000
r(G<->T){all}   0.071088    0.000087    0.053774    0.090039    0.070711   1147.28   1176.29    1.001
pi(A){all}      0.235840    0.000056    0.221331    0.250501    0.235682    980.58   1050.36    1.001
pi(C){all}      0.283686    0.000058    0.269022    0.298605    0.283745   1052.03   1067.05    1.001
pi(G){all}      0.295590    0.000061    0.280983    0.310867    0.295687   1030.87   1034.63    1.000
pi(T){all}      0.184883    0.000042    0.171702    0.196979    0.184711    983.39   1130.93    1.000
alpha{1,2}      0.123627    0.000054    0.110355    0.137989    0.123218   1202.45   1278.73    1.000
alpha{3}        5.268078    1.060271    3.423809    7.391454    5.154518   1257.85   1379.43    1.000
pinvar{all}     0.376826    0.000477    0.333537    0.418400    0.376381    999.65   1187.89    1.001
------------------------------------------------------------------------------------------------------
* 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	-9281.48237
Model 2: PositiveSelection	-9281.482466
Model 0: one-ratio	-9355.132281
Model 3: discrete	-9266.787676
Model 7: beta	-9268.495154
Model 8: beta&w>1	-9264.543014


Model 0 vs 1	147.29982200000086

Model 2 vs 1	1.919999995152466E-4

Model 8 vs 7	7.904279999998835

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_Sudx-PC)

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

    21 T      0.716         1.154
   187 A      0.944         1.448
   324 P      0.981*        1.494

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_Sudx-PC)

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

    21 T      0.794         1.326 +- 0.409
   185 P      0.645         1.155 +- 0.514
   187 A      0.912         1.446 +- 0.299
   233 G      0.691         1.207 +- 0.495
   322 G      0.657         1.168 +- 0.509
   323 P      0.650         1.161 +- 0.512
   324 P      0.956*        1.487 +- 0.244