--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Jan 23 09:44:04 GMT 2020
codeml.models=0 1 2 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=/opt/mrbayes_3.2.2/src
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/data/1res/adhE2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/data/1res/adhE2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/1res/adhE2/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 /data/1res/adhE2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1470.09         -1473.55
2      -1470.11         -1473.29
--------------------------------------
TOTAL    -1470.10         -1473.43
--------------------------------------


Model parameter summaries over the runs sampled in files
"/data/1res/adhE2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/1res/adhE2/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 "/data/1res/adhE2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.897627    0.091383    0.345431    1.506139    0.865571   1302.52   1401.76    1.000
r(A<->C){all}   0.169711    0.020798    0.000085    0.462745    0.131429    237.32    292.57    1.009
r(A<->G){all}   0.171098    0.020941    0.000011    0.461043    0.131861    171.91    195.72    1.000
r(A<->T){all}   0.171830    0.018975    0.000129    0.447164    0.139122    135.22    169.60    1.005
r(C<->G){all}   0.155252    0.018268    0.000026    0.428926    0.117615    205.00    270.61    1.000
r(C<->T){all}   0.158533    0.019276    0.000015    0.445012    0.117438    113.13    181.99    1.000
r(G<->T){all}   0.173576    0.020549    0.000050    0.453254    0.137118    172.37    196.09    1.005
pi(A){all}      0.196143    0.000146    0.172586    0.218871    0.196155   1332.27   1416.64    1.000
pi(C){all}      0.309763    0.000206    0.282501    0.338219    0.309691   1012.62   1232.80    1.000
pi(G){all}      0.311957    0.000192    0.285288    0.338180    0.311749   1402.44   1435.41    1.000
pi(T){all}      0.182137    0.000136    0.160028    0.204982    0.182048   1501.00   1501.00    1.000
alpha{1,2}      0.430139    0.235415    0.000215    1.385599    0.268271    889.56    965.83    1.001
alpha{3}        0.451137    0.227718    0.000548    1.404458    0.295273   1163.63   1218.51    1.000
pinvar{all}     0.998609    0.000003    0.995637    0.999999    0.999134   1284.34   1329.58    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	-1397.230031
Model 2: PositiveSelection	-1397.230031
Model 0: one-ratio	-1397.230031
Model 7: beta	-1397.230031
Model 8: beta&w>1	-1397.230031


Model 0 vs 1	0.0

Model 2 vs 1	0.0

Model 8 vs 7	0.0