--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Nov 08 10:14:39 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/NS5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/ZikaADOPSresults/NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ZikaADOPSresults/NS5/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/NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -10822.54        -10911.88
2     -10821.50        -10898.10
--------------------------------------
TOTAL   -10821.89        -10911.18
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/ZikaADOPSresults/NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/ZikaADOPSresults/NS5/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/NS5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.155229    0.002651    1.060746    1.261226    1.153351    902.26    993.88    1.001
r(A<->C){all}   0.029529    0.000020    0.020922    0.038110    0.029286    758.16    816.36    1.000
r(A<->G){all}   0.219318    0.000317    0.185821    0.254013    0.218515    210.25    288.47    1.002
r(A<->T){all}   0.032351    0.000030    0.021762    0.042626    0.032247    558.18    615.95    1.000
r(C<->G){all}   0.006054    0.000004    0.002344    0.009939    0.005919    780.96    781.29    1.000
r(C<->T){all}   0.690636    0.000436    0.649253    0.730652    0.691614    189.68    274.56    1.002
r(G<->T){all}   0.022112    0.000018    0.013546    0.030113    0.021911    789.62    808.13    1.000
pi(A){all}      0.279567    0.000062    0.264710    0.295412    0.279521    758.11    890.50    1.001
pi(C){all}      0.228286    0.000051    0.214933    0.242902    0.228134    779.29    933.40    1.001
pi(G){all}      0.297594    0.000066    0.282052    0.314153    0.297650    924.53    985.18    1.000
pi(T){all}      0.194553    0.000041    0.181853    0.206784    0.194518    856.13    895.46    1.001
alpha{1,2}      0.142173    0.000085    0.125022    0.160823    0.141804    862.32   1021.63    1.000
alpha{3}        5.201097    1.168830    3.299673    7.295986    5.084695    917.96   1144.41    1.000
pinvar{all}     0.251413    0.000776    0.198892    0.306758    0.252207    879.31    937.91    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	-10452.071124
Model 2: PositiveSelection	-10452.071125
Model 0: one-ratio	-10512.879866
Model 3: discrete	-10442.852466
Model 7: beta	-10444.785115
Model 8: beta&w>1	-10443.15373


Model 0 vs 1	121.61748399999851

Model 2 vs 1	2.0000006770715117E-6

Model 8 vs 7	3.262770000001183