--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Feb 15 19:47:10 WET 2016
codeml.models=
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/Z_B1/Zika-NS3_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_3/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/Z_B1/Zika-NS3_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -5059.60         -5122.33
2      -5058.07         -5119.74
--------------------------------------
TOTAL    -5058.56         -5121.71
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_3/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/Z_B1/Zika-NS3_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.771744    0.004514    0.647474    0.904792    0.768009    585.84    610.81    1.000
r(A<->C){all}   0.028299    0.000054    0.015036    0.042817    0.027756    819.90    887.88    1.000
r(A<->G){all}   0.169378    0.000548    0.130012    0.219954    0.167865    475.46    596.00    1.000
r(A<->T){all}   0.037409    0.000092    0.019134    0.056227    0.036592    854.57    880.90    1.001
r(C<->G){all}   0.012462    0.000030    0.002867    0.022978    0.011892    820.39    865.60    1.000
r(C<->T){all}   0.726158    0.000852    0.672259    0.783187    0.727329    399.08    484.95    1.000
r(G<->T){all}   0.026294    0.000069    0.011298    0.042457    0.025450    708.20    735.01    1.000
pi(A){all}      0.281580    0.000096    0.262478    0.300912    0.281572   1017.03   1044.41    1.000
pi(C){all}      0.232508    0.000077    0.214731    0.249785    0.232481    980.17   1119.45    1.000
pi(G){all}      0.278689    0.000094    0.260907    0.298217    0.278285    835.32    921.59    1.000
pi(T){all}      0.207222    0.000072    0.190225    0.223361    0.207208   1088.20   1205.47    1.000
alpha{1,2}      0.094882    0.000339    0.061249    0.127996    0.097164    604.26    674.08    1.000
alpha{3}        4.536933    1.206159    2.489765    6.534293    4.441817   1312.61   1401.98    1.000
pinvar{all}     0.279117    0.002314    0.184660    0.369486    0.282047    549.95    748.35    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: One dN/dS ratio for branches, 	-4771.449896