--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Feb 17 00:56:01 WET 2016
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=/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/DATA/Zika/B4_A/Zika-NS5_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_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/DATA/Zika/B4_A/Zika-NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -9155.96         -9247.68
2      -9154.07         -9238.00
--------------------------------------
TOTAL    -9154.62         -9246.99
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B4_A/Zika-NS5_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/DATA/Zika/B4_A/Zika-NS5_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}         1.119654    0.003470    1.003076    1.232045    1.117332    714.32    750.83    1.000
r(A<->C){all}   0.023124    0.000020    0.014547    0.031631    0.022844    599.65    717.76    1.000
r(A<->G){all}   0.215361    0.000427    0.175094    0.255568    0.214306    356.15    386.78    1.000
r(A<->T){all}   0.020253    0.000024    0.011388    0.030361    0.019853    630.81    701.16    1.001
r(C<->G){all}   0.003003    0.000003    0.000164    0.006245    0.002767    795.64    818.83    1.000
r(C<->T){all}   0.716584    0.000547    0.670195    0.760399    0.717576    334.65    360.29    1.000
r(G<->T){all}   0.021675    0.000020    0.013935    0.031223    0.021332    682.28    718.14    1.000
pi(A){all}      0.280519    0.000062    0.264520    0.295282    0.280289    924.08   1014.58    1.002
pi(C){all}      0.227629    0.000052    0.213053    0.241120    0.227444    908.07    995.75    1.002
pi(G){all}      0.295418    0.000068    0.278933    0.311877    0.295459    979.54   1032.45    1.000
pi(T){all}      0.196434    0.000045    0.182725    0.208846    0.196381    684.82    887.79    1.000
alpha{1,2}      0.116468    0.000068    0.101205    0.133228    0.116085   1166.94   1190.04    1.000
alpha{3}        5.063851    1.150929    3.116586    7.164913    4.963227   1238.93   1344.24    1.000
pinvar{all}     0.303283    0.000726    0.248076    0.353593    0.303840    724.25    913.15    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	-8535.980608
Model 2: PositiveSelection	-8535.980632
Model 0: one-ratio	-8571.24262
Model 3: discrete	-8529.52584
Model 7: beta	-8529.594999
Model 8: beta&w>1	-8529.595061


Model 0 vs 1	70.5240240000021

Model 2 vs 1	4.8000001697801054E-5

Model 8 vs 7	1.2399999832268804E-4