--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Oct 28 06:00:26 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/Ebola_B1_2/VP40/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1_2/VP40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/VP40/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/Ebola_B1_2/VP40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -6554.53         -6601.94
2      -6550.76         -6599.98
--------------------------------------
TOTAL    -6551.43         -6601.38
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1_2/VP40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1_2/VP40/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/Ebola_B1_2/VP40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         4.570179    0.106992    3.942134    5.198495    4.550034    650.73    780.96    1.000
r(A<->C){all}   0.130904    0.000231    0.103766    0.163054    0.130414   1011.18   1032.10    1.002
r(A<->G){all}   0.383981    0.000838    0.329177    0.440463    0.383506    563.09    694.39    1.000
r(A<->T){all}   0.057341    0.000182    0.031586    0.082838    0.056619    638.04    667.94    1.001
r(C<->G){all}   0.007950    0.000047    0.000001    0.021419    0.006165    837.57    856.76    1.000
r(C<->T){all}   0.357009    0.000782    0.301381    0.411328    0.356658    615.56    690.22    1.000
r(G<->T){all}   0.062815    0.000188    0.038233    0.090299    0.062217    700.35    741.38    1.000
pi(A){all}      0.270731    0.000076    0.254692    0.288760    0.270501    905.75    919.35    1.001
pi(C){all}      0.270998    0.000077    0.254142    0.288079    0.270995    910.06    935.40    1.000
pi(G){all}      0.226358    0.000071    0.210334    0.243713    0.226414   1005.55   1076.59    1.000
pi(T){all}      0.231912    0.000070    0.215531    0.247979    0.231723   1009.89   1112.30    1.000
alpha{1,2}      0.165895    0.000126    0.143891    0.187268    0.165103   1033.11   1091.52    1.000
alpha{3}        4.140493    0.855780    2.522022    5.948563    4.022639   1116.81   1174.84    1.000
pinvar{all}     0.031809    0.000332    0.000116    0.066286    0.029833   1163.53   1272.61    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	-4996.181233
Model 2: PositiveSelection	-4996.181233
Model 0: one-ratio	-5066.591126
Model 3: discrete	-4958.357556
Model 7: beta	-4961.765258
Model 8: beta&w>1	-4961.765895


Model 0 vs 1	140.81978600000002

Model 2 vs 1	0.0

Model 8 vs 7	0.001273999998375075