--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Feb 15 18:40:10 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4290.12         -4344.83
2      -4288.75         -4358.34
--------------------------------------
TOTAL    -4289.22         -4357.65
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Z_B1/Zika-NS3_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.903752    0.012935    0.705603    1.143963    0.891314    387.28    420.76    1.000
r(A<->C){all}   0.019023    0.000052    0.006685    0.033874    0.018367    521.16    609.38    1.001
r(A<->G){all}   0.268087    0.001994    0.189393    0.362198    0.266993    310.27    431.65    1.000
r(A<->T){all}   0.015838    0.000057    0.002340    0.030218    0.014681    541.64    707.15    1.000
r(C<->G){all}   0.006916    0.000018    0.000484    0.015554    0.006160    873.43    891.48    1.000
r(C<->T){all}   0.664737    0.002362    0.563381    0.752409    0.665257    294.56    395.27    1.000
r(G<->T){all}   0.025398    0.000080    0.009583    0.043789    0.024597    750.64    818.10    1.000
pi(A){all}      0.281122    0.000099    0.261962    0.300419    0.281192   1050.74   1182.86    1.000
pi(C){all}      0.230149    0.000086    0.212020    0.247698    0.230138    881.59    970.07    1.000
pi(G){all}      0.280475    0.000096    0.261942    0.300056    0.280172   1075.68   1127.92    1.002
pi(T){all}      0.208255    0.000075    0.192267    0.225421    0.208298   1044.24   1169.25    1.000
alpha{1,2}      0.041711    0.000522    0.000168    0.075718    0.043404   1088.72   1108.40    1.000
alpha{3}        3.603297    0.972820    1.874561    5.533610    3.468452   1183.99   1279.52    1.000
pinvar{all}     0.451326    0.000972    0.389857    0.510911    0.451929   1346.32   1360.00    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, 	-4021.142799