--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Nov 08 10:32:55 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/ZikaADOPSresults/pr/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1       -941.72          -979.63
2       -941.91          -984.24
--------------------------------------
TOTAL     -941.81          -983.56
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.284241    0.071519    0.819832    1.798684    1.243649    533.06    719.34    1.002
r(A<->C){all}   0.052870    0.000491    0.014432    0.096465    0.050331    651.63    694.94    1.003
r(A<->G){all}   0.182709    0.003526    0.076589    0.300048    0.176887    362.76    393.55    1.000
r(A<->T){all}   0.016335    0.000170    0.000001    0.040703    0.013252    439.45    587.58    1.000
r(C<->G){all}   0.009389    0.000078    0.000003    0.026448    0.006890    744.40    819.67    1.000
r(C<->T){all}   0.716030    0.005516    0.565985    0.850447    0.720446    333.78    384.20    1.001
r(G<->T){all}   0.022666    0.000152    0.002607    0.047007    0.020660    362.65    614.03    1.000
pi(A){all}      0.261494    0.000570    0.216056    0.308144    0.260412   1076.43   1094.60    1.000
pi(C){all}      0.215484    0.000519    0.173447    0.261379    0.215106    513.09    822.57    1.000
pi(G){all}      0.290855    0.000629    0.239508    0.336884    0.291105   1099.73   1165.36    1.000
pi(T){all}      0.232167    0.000543    0.189275    0.279048    0.231033    968.25   1088.37    1.000
alpha{1,2}      0.160170    0.001649    0.091637    0.245280    0.155157   1114.69   1175.96    1.000
alpha{3}        1.655989    0.479472    0.530707    3.007114    1.530987    996.14    998.82    1.001
pinvar{all}     0.210514    0.009180    0.009376    0.365474    0.216725    893.98    927.94    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	-913.421485
Model 2: PositiveSelection	-913.421485
Model 0: one-ratio	-915.624986
Model 3: discrete	-911.681233
Model 7: beta	-912.031149
Model 8: beta&w>1	-912.031209


Model 0 vs 1	4.407002000000148

Model 2 vs 1	0.0

Model 8 vs 7	1.199999999244028E-4