--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Nov 24 18:34:29 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/330/nub-PE/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/330/nub-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/330/nub-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/330/nub-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7038.70         -7057.51
2      -7038.74         -7056.74
--------------------------------------
TOTAL    -7038.72         -7057.20
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/330/nub-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/330/nub-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/330/nub-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}         1.402177    0.007245    1.227311    1.562600    1.398611   1252.28   1303.42    1.000
r(A<->C){all}   0.094727    0.000166    0.069205    0.119456    0.094140    973.65   1149.44    1.000
r(A<->G){all}   0.246305    0.000501    0.202788    0.288942    0.245762    904.35    944.31    1.000
r(A<->T){all}   0.098958    0.000352    0.064352    0.136315    0.098154    815.97    997.81    1.002
r(C<->G){all}   0.063589    0.000079    0.047401    0.081289    0.063062   1201.00   1276.20    1.000
r(C<->T){all}   0.403644    0.000660    0.349899    0.449057    0.403747    619.83    721.69    1.001
r(G<->T){all}   0.092777    0.000181    0.066518    0.119633    0.092097    838.66    958.36    1.000
pi(A){all}      0.213507    0.000079    0.197138    0.231316    0.213476   1144.77   1146.20    1.003
pi(C){all}      0.342693    0.000098    0.323965    0.362298    0.342462   1073.24   1085.68    1.000
pi(G){all}      0.275746    0.000091    0.256901    0.294349    0.275820   1098.10   1196.08    1.000
pi(T){all}      0.168054    0.000057    0.152909    0.182651    0.168034    901.73    973.42    1.001
alpha{1,2}      0.138204    0.000109    0.117970    0.158458    0.137600   1347.47   1376.70    1.000
alpha{3}        4.251027    0.918673    2.508134    6.103159    4.121715   1501.00   1501.00    1.000
pinvar{all}     0.380780    0.000752    0.326954    0.433317    0.381218   1325.56   1398.15    1.002
------------------------------------------------------------------------------------------------------
* 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	-6197.207384
Model 2: PositiveSelection	-6197.207427
Model 0: one-ratio	-6263.357076
Model 3: discrete	-6178.036014
Model 7: beta	-6181.068485
Model 8: beta&w>1	-6178.071412


Model 0 vs 1	132.29938399999992

Model 2 vs 1	8.600000001024455E-5

Model 8 vs 7	5.994145999999091

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_nub-PE)

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

   156 T      0.976*        1.519
   321 T      0.806         1.303
   330 I      0.812         1.309

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_nub-PE)

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

   156 T      0.963*        1.556 +- 0.405
   321 T      0.833         1.418 +- 0.467
   330 I      0.865         1.443 +- 0.432
   379 S      0.586         1.130 +- 0.492