--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Oct 08 21:15:53 WEST 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=/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/B2_A/Zika-NS1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/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/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4274.14         -4360.36
2      -4319.81         -4396.65
--------------------------------------
TOTAL    -4274.83         -4395.96
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_5/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/B2_A/Zika-NS1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        14.238639    2.011118   11.393440   17.073970   14.172340    123.09    343.90    1.070
r(A<->C){all}   0.010970    0.000109    0.000395    0.029331    0.005482    247.52    247.72    3.591
r(A<->G){all}   0.079640    0.006165    0.004784    0.214303    0.058973     90.18    128.89    3.726
r(A<->T){all}   0.013052    0.000141    0.000771    0.033858    0.006762    160.89    180.43    3.465
r(C<->G){all}   0.004127    0.000018    0.000060    0.012472    0.001907    251.66    380.67    2.302
r(C<->T){all}   0.883697    0.011859    0.702386    0.991429    0.902717     87.99    112.25    4.296
r(G<->T){all}   0.008513    0.000066    0.000414    0.023799    0.004256    191.09    251.83    2.778
pi(A){all}      0.292165    0.000175    0.266018    0.318110    0.291963    385.16    553.53    1.008
pi(C){all}      0.214210    0.000132    0.189858    0.234657    0.214215    304.72    655.91    1.056
pi(G){all}      0.291395    0.000180    0.265212    0.317405    0.290804    297.79    546.58    1.016
pi(T){all}      0.202230    0.000118    0.180089    0.223212    0.201853    240.08    553.75    1.040
alpha{1,2}      0.068491    0.000028    0.058976    0.078069    0.068455    340.42    385.08    1.954
alpha{3}        0.404961    0.021970    0.230589    0.595740    0.326821    166.95    256.63    7.642
pinvar{all}     0.314600    0.002943    0.222890    0.421031    0.310498    259.54    442.40    1.978
------------------------------------------------------------------------------------------------------
* 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	-3617.64223
Model 2: PositiveSelection	-3617.64223
Model 0: one-ratio	-3623.248625
Model 3: discrete	-3609.543119
Model 7: beta	-3610.243602
Model 8: beta&w>1	-3610.244129


Model 0 vs 1	11.212790000000496

Model 2 vs 1	0.0

Model 8 vs 7	0.0010540000002947636