--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Nov 05 02:01:55 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/vp24/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp24/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/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3891.89         -3922.79
2      -3891.51         -3919.53
--------------------------------------
TOTAL    -3891.68         -3922.13
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp24/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/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.054835    0.105412    3.454792    4.714971    4.038131    961.18   1019.30    1.000
r(A<->C){all}   0.133750    0.000377    0.096895    0.171654    0.133364    841.57    888.40    1.000
r(A<->G){all}   0.304961    0.000907    0.243142    0.361515    0.304498    789.35    845.13    1.000
r(A<->T){all}   0.046135    0.000168    0.022236    0.071692    0.045258   1044.70   1047.72    1.000
r(C<->G){all}   0.017873    0.000108    0.000463    0.037294    0.016303    750.80    906.75    1.000
r(C<->T){all}   0.440652    0.001157    0.377534    0.507445    0.440138    741.63    785.49    1.000
r(G<->T){all}   0.056629    0.000194    0.031199    0.084487    0.055954   1067.58   1099.13    1.000
pi(A){all}      0.291027    0.000160    0.265597    0.314791    0.290737   1064.26   1089.46    1.000
pi(C){all}      0.230445    0.000118    0.209504    0.252417    0.230240    857.74   1009.58    1.000
pi(G){all}      0.207558    0.000128    0.185192    0.228653    0.207540    666.61    915.96    1.000
pi(T){all}      0.270970    0.000149    0.245140    0.293228    0.270866   1006.38   1116.96    1.000
alpha{1,2}      0.165518    0.000209    0.139985    0.196007    0.164526   1144.95   1268.60    1.000
alpha{3}        4.252383    1.069604    2.389553    6.254538    4.120725   1329.98   1404.12    1.000
pinvar{all}     0.037214    0.000535    0.000036    0.079521    0.034796   1314.97   1407.98    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	-3566.059905
Model 2: PositiveSelection	-3566.059905
Model 0: one-ratio	-3589.271015
Model 3: discrete	-3544.960047
Model 7: beta	-3547.782422
Model 8: beta&w>1	-3545.823393


Model 0 vs 1	46.42221999999947

Model 2 vs 1	0.0

Model 8 vs 7	3.918058000000201