--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Nov 05 06:00:17 WET 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=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/Ebolaaminoresults/vp35/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp35/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/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -5647.39         -5682.83
2      -5647.58         -5685.17
--------------------------------------
TOTAL    -5647.48         -5684.57
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp35/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/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.390524    0.106451    3.815348    5.067019    4.380022    758.61    817.83    1.000
r(A<->C){all}   0.096736    0.000227    0.067460    0.126552    0.096330    803.28    885.90    1.001
r(A<->G){all}   0.379942    0.000894    0.323439    0.436753    0.378891    711.15    727.13    1.001
r(A<->T){all}   0.065118    0.000159    0.039865    0.088824    0.064854    984.45    987.69    1.001
r(C<->G){all}   0.016982    0.000100    0.000832    0.036035    0.015748    770.05    906.22    1.001
r(C<->T){all}   0.385830    0.000898    0.326438    0.442239    0.385809    676.48    747.90    1.001
r(G<->T){all}   0.055392    0.000194    0.028628    0.082754    0.054977    799.81    802.77    1.001
pi(A){all}      0.329823    0.000111    0.309499    0.350440    0.329755    855.79    946.28    1.000
pi(C){all}      0.231115    0.000087    0.212948    0.249007    0.231157    770.61    897.13    1.001
pi(G){all}      0.200227    0.000077    0.183488    0.217448    0.200105    991.86   1010.61    1.000
pi(T){all}      0.238835    0.000091    0.220368    0.257414    0.238710   1119.16   1130.32    1.000
alpha{1,2}      0.200565    0.000255    0.171117    0.232789    0.199559   1010.29   1175.20    1.000
alpha{3}        4.284052    0.959495    2.629606    6.271498    4.174216   1180.99   1267.07    1.000
pinvar{all}     0.017900    0.000179    0.000001    0.043691    0.015084    986.04   1186.90    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	-5099.552346
Model 2: PositiveSelection	-5099.552346
Model 0: one-ratio	-5228.980528
Model 3: discrete	-5055.113527
Model 7: beta	-5055.916397
Model 8: beta&w>1	-5055.916487


Model 0 vs 1	258.8563639999993

Model 2 vs 1	0.0

Model 8 vs 7	1.8000000090978574E-4