--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Feb 15 19:08:31 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_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4402.80         -4466.05
2      -4404.47         -4462.07
--------------------------------------
TOTAL    -4403.32         -4465.37
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.982999    0.013908    0.777034    1.222952    0.971574    410.29    459.15    1.001
r(A<->C){all}   0.025146    0.000067    0.010116    0.041506    0.024460    640.81    645.74    1.000
r(A<->G){all}   0.299723    0.002002    0.219048    0.390608    0.297725    451.45    475.88    1.002
r(A<->T){all}   0.015869    0.000061    0.002011    0.030487    0.014829    608.66    670.29    1.000
r(C<->G){all}   0.004831    0.000014    0.000004    0.012245    0.003896    788.01    874.39    1.001
r(C<->T){all}   0.637476    0.002160    0.546507    0.727567    0.639326    432.81    455.65    1.002
r(G<->T){all}   0.016955    0.000055    0.003709    0.031524    0.015880    770.95    771.99    1.001
pi(A){all}      0.283263    0.000098    0.263535    0.301518    0.283373   1028.56   1079.58    1.000
pi(C){all}      0.232230    0.000083    0.214209    0.250014    0.232116   1123.40   1156.76    1.000
pi(G){all}      0.279925    0.000095    0.259403    0.297168    0.279763   1106.60   1244.93    1.001
pi(T){all}      0.204583    0.000074    0.188206    0.221631    0.204724   1008.95   1090.89    1.001
alpha{1,2}      0.035676    0.000436    0.000102    0.068462    0.035970    834.34    927.19    1.000
alpha{3}        3.547942    0.860756    1.986264    5.320641    3.447681   1383.34   1442.17    1.000
pinvar{all}     0.437282    0.000975    0.378356    0.498432    0.438521    988.00   1154.01    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, 	-4152.689471