--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Nov 05 04:17:51 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/vp30/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp30/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp30/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/vp30/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4751.12         -4780.50
2      -4747.23         -4781.31
--------------------------------------
TOTAL    -4747.90         -4780.99
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp30/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp30/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/vp30/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.356307    0.130923    3.672846    5.063989    4.344487    850.95   1054.60    1.000
r(A<->C){all}   0.136041    0.000347    0.100679    0.172930    0.135140    769.16    809.06    1.001
r(A<->G){all}   0.354106    0.001031    0.293495    0.420005    0.353335    858.83    889.57    1.000
r(A<->T){all}   0.043842    0.000142    0.022236    0.067581    0.043201    890.52    922.05    1.000
r(C<->G){all}   0.019826    0.000150    0.000168    0.042538    0.018121    938.98   1028.91    1.000
r(C<->T){all}   0.389274    0.000984    0.327785    0.451094    0.388475    915.40    940.94    1.000
r(G<->T){all}   0.056911    0.000195    0.032064    0.084312    0.056006    906.58   1007.68    1.000
pi(A){all}      0.326458    0.000134    0.303177    0.348258    0.326550   1052.65   1097.63    1.000
pi(C){all}      0.217235    0.000095    0.198753    0.236868    0.217209    756.31    865.18    1.000
pi(G){all}      0.197941    0.000103    0.178776    0.217571    0.197863    760.84    814.94    1.000
pi(T){all}      0.258366    0.000124    0.235834    0.278525    0.258145   1146.34   1158.38    1.000
alpha{1,2}      0.225329    0.000469    0.185093    0.268446    0.223980   1050.25   1275.62    1.000
alpha{3}        4.191909    0.982136    2.389737    6.100594    4.075852   1356.08   1428.54    1.000
pinvar{all}     0.031281    0.000403    0.000018    0.067993    0.029013   1250.59   1368.20    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	-4260.659656
Model 2: PositiveSelection	-4260.659656
Model 0: one-ratio	-4322.602681
Model 3: discrete	-4206.815233
Model 7: beta	-4206.99123
Model 8: beta&w>1	-4206.878591


Model 0 vs 1	123.88605000000098

Model 2 vs 1	0.0

Model 8 vs 7	0.2252779999998893