--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 25 14:38:42 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/1/14-3-3zeta-PH/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/1/14-3-3zeta-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/14-3-3zeta-PH/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/1/14-3-3zeta-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1543.62         -1567.77
2      -1544.11         -1563.81
--------------------------------------
TOTAL    -1543.84         -1567.10
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/1/14-3-3zeta-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/14-3-3zeta-PH/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/1/14-3-3zeta-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.246494    0.001602    0.173031    0.324009    0.242767   1103.27   1122.88    1.000
r(A<->C){all}   0.111299    0.001137    0.051950    0.178245    0.107781    894.11    919.19    1.000
r(A<->G){all}   0.154615    0.001757    0.080753    0.237992    0.150392    694.22    813.52    1.000
r(A<->T){all}   0.065836    0.000992    0.010529    0.126475    0.061315    639.84    780.68    1.001
r(C<->G){all}   0.063359    0.000685    0.018397    0.115967    0.059883    966.47   1016.17    1.000
r(C<->T){all}   0.555121    0.004818    0.424696    0.693123    0.555175    577.68    640.20    1.000
r(G<->T){all}   0.049770    0.000752    0.007372    0.103628    0.044993    795.45    824.71    1.000
pi(A){all}      0.286651    0.000249    0.256314    0.317695    0.286463   1034.46   1123.43    1.000
pi(C){all}      0.261095    0.000240    0.232054    0.291559    0.260862   1223.63   1349.92    1.001
pi(G){all}      0.257423    0.000243    0.226461    0.286314    0.257530   1180.10   1329.71    1.003
pi(T){all}      0.194831    0.000186    0.168107    0.220922    0.194652   1170.56   1249.17    1.000
alpha{1,2}      0.057616    0.001809    0.000105    0.133641    0.051188    951.75   1130.46    1.000
alpha{3}        2.056245    0.633411    0.705016    3.648509    1.921707   1236.79   1368.89    1.000
pinvar{all}     0.475315    0.008296    0.295716    0.642704    0.485554    870.98   1115.57    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	-1451.36118
Model 2: PositiveSelection	-1451.36118
Model 0: one-ratio	-1458.92382
Model 3: discrete	-1451.332921
Model 7: beta	-1451.333746
Model 8: beta&w>1	-1451.361179


Model 0 vs 1	15.125279999999748

Model 2 vs 1	0.0

Model 8 vs 7	0.054865999999947235