--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Oct 06 16:46:10 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_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_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/DATA/Zika/B2_A/Zika-NS1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4400.59         -4478.35
2      -4408.29         -4474.69
--------------------------------------
TOTAL    -4401.29         -4477.69
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B2_A/Zika-NS1_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/DATA/Zika/B2_A/Zika-NS1_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}        16.597211    2.478963   13.281510   19.474140   16.584730    356.34    387.59    1.001
r(A<->C){all}   0.026546    0.000053    0.013402    0.040819    0.025981    648.22    748.63    1.000
r(A<->G){all}   0.239647    0.001070    0.171298    0.299298    0.240774    159.86    192.33    1.002
r(A<->T){all}   0.031999    0.000072    0.016073    0.048187    0.031269    546.37    578.66    1.005
r(C<->G){all}   0.009031    0.000020    0.001253    0.017680    0.008285    540.18    665.27    1.000
r(C<->T){all}   0.674728    0.001412    0.605575    0.751826    0.673377    155.40    180.76    1.003
r(G<->T){all}   0.018049    0.000042    0.006223    0.030744    0.017317    559.50    626.88    1.000
pi(A){all}      0.289597    0.000177    0.264320    0.316037    0.289718    685.54    801.18    1.000
pi(C){all}      0.210774    0.000124    0.189478    0.232885    0.209951    773.15    867.98    1.000
pi(G){all}      0.298133    0.000181    0.272789    0.325806    0.298033    783.76    866.62    1.000
pi(T){all}      0.201496    0.000120    0.180706    0.223696    0.201413    793.24    847.52    1.000
alpha{1,2}      0.068706    0.000008    0.063635    0.074519    0.068549    534.84    592.78    1.000
alpha{3}        0.258719    0.000183    0.233074    0.284629    0.257990    396.63    480.58    1.003
pinvar{all}     0.381221    0.001193    0.307439    0.441371    0.382288    695.59    785.96    1.001
------------------------------------------------------------------------------------------------------
* 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	-3654.418098
Model 2: PositiveSelection	-3654.418098
Model 0: one-ratio	-3661.213426
Model 3: discrete	-3647.050595
Model 7: beta	-3647.77356
Model 8: beta&w>1	-3647.775811


Model 0 vs 1	13.590655999999399

Model 2 vs 1	0.0

Model 8 vs 7	0.004501999999774853