--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 07 12:06:05 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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/ADOPS1/Zikaomegamapresults/NS3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Zikaomegamapresults/NS3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zikaomegamapresults/NS3/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/ADOPS1/Zikaomegamapresults/NS3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -6667.04         -6721.40
2      -6667.36         -6716.36
--------------------------------------
TOTAL    -6667.19         -6720.72
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Zikaomegamapresults/NS3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zikaomegamapresults/NS3/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/ADOPS1/Zikaomegamapresults/NS3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.986945    0.003234    0.877329    1.093764    0.984761   1121.56   1271.91    1.000
r(A<->C){all}   0.027642    0.000033    0.016475    0.038272    0.027280    817.57    937.67    1.000
r(A<->G){all}   0.185669    0.000391    0.149932    0.226149    0.184579    510.94    557.00    1.000
r(A<->T){all}   0.039323    0.000053    0.026448    0.054140    0.038636    914.55    971.25    1.000
r(C<->G){all}   0.020315    0.000026    0.010691    0.030139    0.019927    902.89    928.97    1.001
r(C<->T){all}   0.685568    0.000624    0.636590    0.733401    0.686288    463.45    510.58    1.000
r(G<->T){all}   0.041484    0.000059    0.027341    0.056635    0.040790    740.08    793.43    1.000
pi(A){all}      0.280754    0.000097    0.261049    0.299069    0.280520    930.55   1065.88    1.000
pi(C){all}      0.229590    0.000076    0.213709    0.247104    0.229665   1004.18   1084.28    1.000
pi(G){all}      0.280983    0.000095    0.263454    0.300996    0.280864    906.98   1076.48    1.000
pi(T){all}      0.208673    0.000070    0.192853    0.225612    0.208679   1046.40   1147.66    1.000
alpha{1,2}      0.136515    0.000137    0.116085    0.160284    0.136054    998.60   1113.86    1.000
alpha{3}        4.522827    1.051938    2.724199    6.586011    4.408111   1176.54   1338.77    1.000
pinvar{all}     0.258966    0.001324    0.186359    0.325988    0.260131   1058.20   1133.02    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	-6403.791453
Model 2: PositiveSelection	-6403.791454
Model 0: one-ratio	-6421.477267
Model 3: discrete	-6397.236881
Model 7: beta	-6397.328339
Model 8: beta&w>1	-6397.328595


Model 0 vs 1	35.37162800000078

Model 2 vs 1	2.0000006770715117E-6

Model 8 vs 7	5.120000005263137E-4