--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Oct 07 10:06:18 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/B3_A/Zika-NS4B_4/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/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/B3_A/Zika-NS4B_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3440.23         -3531.67
2      -3427.91         -3537.37
--------------------------------------
TOTAL    -3428.60         -3536.68
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/B3_A/Zika-NS4B_4/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/B3_A/Zika-NS4B_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        14.463763    3.367703   11.043170   18.079690   14.431530     36.11    220.50    1.318
r(A<->C){all}   0.014426    0.000123    0.000911    0.033546    0.014934      8.56    152.09    1.812
r(A<->G){all}   0.138885    0.012118    0.006894    0.297569    0.166220      8.11     44.22    2.249
r(A<->T){all}   0.034723    0.000617    0.002916    0.072461    0.040509      8.11    245.54    2.058
r(C<->G){all}   0.006844    0.000044    0.000005    0.019511    0.005562      9.55    269.35    1.539
r(C<->T){all}   0.785889    0.025684    0.568984    0.983941    0.729624      7.89     44.87    2.415
r(G<->T){all}   0.019233    0.000222    0.001005    0.044535    0.019667      9.58    254.20    1.910
pi(A){all}      0.258666    0.000240    0.230279    0.291155    0.258204    174.88    479.25    1.020
pi(C){all}      0.254453    0.000203    0.226481    0.281439    0.254350    168.19    551.45    1.015
pi(G){all}      0.260562    0.000236    0.229451    0.290288    0.260112    255.94    467.28    1.000
pi(T){all}      0.226318    0.000192    0.199115    0.253216    0.226236    149.61    478.51    1.000
alpha{1,2}      0.073364    0.000018    0.064645    0.081345    0.073445     31.15    285.15    1.143
alpha{3}        0.359665    0.014423    0.240636    0.600695    0.297884     21.22    301.76    1.633
pinvar{all}     0.237046    0.007041    0.063674    0.374678    0.249203     19.97    112.20    1.682
------------------------------------------------------------------------------------------------------
* 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	-2931.977441
Model 2: PositiveSelection	-2931.977339
Model 0: one-ratio	-2968.77852
Model 3: discrete	-2931.933343
Model 7: beta	-2935.281734
Model 8: beta&w>1	-2935.283846


Model 0 vs 1	73.60215799999969

Model 2 vs 1	2.0399999993969686E-4

Model 8 vs 7	0.004223999999339867