--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Nov 05 07:36:45 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/vp40/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/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/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -6286.82         -6321.29
2      -6287.20         -6315.91
--------------------------------------
TOTAL    -6286.99         -6320.61
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/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/ADOPS1/Ebolaaminoresults/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}         4.047650    0.093518    3.482754    4.652256    4.038287    909.71   1119.77    1.000
r(A<->C){all}   0.123958    0.000245    0.096810    0.157824    0.123320    966.44   1038.56    1.001
r(A<->G){all}   0.385542    0.000805    0.327096    0.437811    0.385541    690.27    777.39    1.000
r(A<->T){all}   0.061770    0.000209    0.034669    0.090605    0.060942    667.14    790.18    1.000
r(C<->G){all}   0.008225    0.000049    0.000001    0.022351    0.006529    728.30    850.79    1.000
r(C<->T){all}   0.355778    0.000784    0.300188    0.408550    0.354920    932.44    934.00    1.001
r(G<->T){all}   0.064727    0.000197    0.037525    0.090991    0.064022    961.59   1007.77    1.000
pi(A){all}      0.270993    0.000077    0.252723    0.287538    0.270824   1131.15   1189.53    1.000
pi(C){all}      0.271410    0.000079    0.254947    0.290143    0.271688   1113.05   1181.10    1.000
pi(G){all}      0.226877    0.000072    0.210325    0.243526    0.226839   1208.63   1269.77    1.000
pi(T){all}      0.230720    0.000069    0.215884    0.247529    0.230548    939.66    946.95    1.000
alpha{1,2}      0.166748    0.000143    0.143714    0.189751    0.165813    938.88   1103.77    1.000
alpha{3}        3.993471    0.811470    2.358286    5.757092    3.880608   1394.17   1447.58    1.000
pinvar{all}     0.035730    0.000455    0.000016    0.073194    0.033683   1460.73   1480.86    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	-4769.53679
Model 2: PositiveSelection	-4769.53679
Model 0: one-ratio	-4841.668108
Model 3: discrete	-4734.507062
Model 7: beta	-4737.765685
Model 8: beta&w>1	-4737.766103


Model 0 vs 1	144.26263599999947

Model 2 vs 1	0.0

Model 8 vs 7	8.35999999253545E-4