--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Nov 06 17:35:10 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/E/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -5848.52         -5915.94
2      -5845.71         -5905.07
--------------------------------------
TOTAL    -5846.34         -5915.25
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.133307    0.005177    0.994493    1.278667    1.132369    861.87    966.70    1.000
r(A<->C){all}   0.030545    0.000044    0.018127    0.043413    0.030059    858.95    871.15    1.000
r(A<->G){all}   0.163993    0.000468    0.120537    0.203859    0.162416    326.95    383.81    1.002
r(A<->T){all}   0.034608    0.000057    0.021110    0.049862    0.034148    668.60    716.70    1.000
r(C<->G){all}   0.021679    0.000031    0.011621    0.032941    0.021169    704.21    821.66    1.000
r(C<->T){all}   0.720793    0.000783    0.665378    0.773396    0.722229    302.12    334.85    1.002
r(G<->T){all}   0.028383    0.000042    0.016420    0.041449    0.028098    745.26    748.22    1.000
pi(A){all}      0.262595    0.000109    0.240664    0.281603    0.262395    812.25    909.88    1.002
pi(C){all}      0.232886    0.000091    0.215850    0.252868    0.232893    944.55   1118.86    1.000
pi(G){all}      0.280738    0.000119    0.258213    0.300637    0.280894    709.23    909.74    1.000
pi(T){all}      0.223781    0.000086    0.206455    0.242775    0.223708    980.33   1018.73    1.000
alpha{1,2}      0.164407    0.000210    0.138357    0.195143    0.163339   1081.91   1176.46    1.000
alpha{3}        3.755622    0.926429    2.123162    5.680947    3.645178   1427.04   1464.02    1.002
pinvar{all}     0.247361    0.001527    0.172606    0.324963    0.247737    866.32    993.96    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	-5514.964793
Model 2: PositiveSelection	-5515.564412
Model 0: one-ratio	-5515.564658
Model 3: discrete	-5509.224666
Model 7: beta	-5509.941309
Model 8: beta&w>1	-5509.946172


Model 0 vs 1	1.1997300000002724

Model 2 vs 1	1.1992379999992409

Model 8 vs 7	0.009726000000227941