--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 07 03:26:49 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/Zikaomegamapresults/NS1/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zikaomegamapresults/NS1/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/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4376.66         -4546.23
2      -4376.38         -4530.74
--------------------------------------
TOTAL    -4376.51         -4545.53
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zikaomegamapresults/NS1/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/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         2.098115    0.687712    1.336889    4.039509    1.756498     12.15     13.04    1.047
r(A<->C){all}   0.016865    0.000040    0.004876    0.028354    0.016897     20.56     31.92    1.036
r(A<->G){all}   0.111393    0.001376    0.034540    0.166740    0.119568     13.73     17.06    1.064
r(A<->T){all}   0.017820    0.000046    0.005320    0.030238    0.017690     20.24     32.57    1.034
r(C<->G){all}   0.008134    0.000016    0.001585    0.015943    0.007554     42.84     83.76    1.022
r(C<->T){all}   0.827348    0.002742    0.752118    0.937947    0.814481     13.40     16.30    1.066
r(G<->T){all}   0.018440    0.000043    0.005989    0.030749    0.018264     27.64     39.31    1.031
pi(A){all}      0.278333    0.000158    0.252525    0.301664    0.277975    234.30    410.08    1.000
pi(C){all}      0.222977    0.000124    0.201604    0.244600    0.222695    587.44    661.82    1.001
pi(G){all}      0.283955    0.000163    0.258674    0.308171    0.284026    671.65    672.44    1.000
pi(T){all}      0.214735    0.000122    0.192840    0.235669    0.214878    167.44    284.21    1.001
alpha{1,2}      0.121763    0.000223    0.091607    0.149307    0.122668     19.80     27.14    1.028
alpha{3}        2.304199    0.970799    0.515733    3.927971    2.342646     19.04     24.56    1.048
pinvar{all}     0.166874    0.001484    0.086596    0.238748    0.167303    541.37    787.88    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	-4230.377484
Model 2: PositiveSelection	-4230.377484
Model 0: one-ratio	-4250.007631
Model 3: discrete	-4224.94038
Model 7: beta	-4225.062473
Model 8: beta&w>1	-4225.062647


Model 0 vs 1	39.26029400000152

Model 2 vs 1	0.0

Model 8 vs 7	3.479999995761318E-4