--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Oct 01 00:01:48 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=
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-pr/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-pr/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-pr/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/DATA/Zika/Batch_1_ADOPS/Zika-pr/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1481.10         -1543.08
2      -1485.10         -1536.53
--------------------------------------
TOTAL    -1481.77         -1542.39
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-pr/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/DATA/Zika/Batch_1_ADOPS/Zika-pr/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/DATA/Zika/Batch_1_ADOPS/Zika-pr/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}        14.231963    1.678351   11.762970   16.860310   14.190420    933.64   1023.20    1.001
r(A<->C){all}   0.065258    0.000499    0.022748    0.108233    0.063034    625.73    676.05    1.000
r(A<->G){all}   0.279692    0.003585    0.172386    0.401717    0.277969    269.74    386.90    1.003
r(A<->T){all}   0.038043    0.000241    0.011182    0.068969    0.036023    717.87    734.73    1.000
r(C<->G){all}   0.010499    0.000071    0.000018    0.027123    0.008486    714.40    788.34    1.000
r(C<->T){all}   0.582008    0.004420    0.450093    0.709147    0.583276    273.11    365.03    1.003
r(G<->T){all}   0.024501    0.000118    0.005836    0.045555    0.022937    730.84    739.12    1.002
pi(A){all}      0.280625    0.000597    0.236761    0.332002    0.279752    766.99    917.04    1.000
pi(C){all}      0.205546    0.000434    0.165678    0.246583    0.204474    483.94    728.75    1.001
pi(G){all}      0.288735    0.000589    0.243707    0.338181    0.288211   1028.29   1062.03    1.002
pi(T){all}      0.225094    0.000508    0.184942    0.272649    0.224367    712.00    824.16    1.000
alpha{1,2}      0.083988    0.000026    0.073554    0.093405    0.083735   1185.65   1189.14    1.001
alpha{3}        0.320268    0.002857    0.251928    0.429815    0.318345    186.78    703.29    1.014
pinvar{all}     0.178474    0.003923    0.054999    0.295093    0.179513    885.70    994.27    1.004
------------------------------------------------------------------------------------------------------
* 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	-1242.129723
Model 2: PositiveSelection	-1242.13823
Model 0: one-ratio	-1242.13823
Model 3: discrete	-1237.217799
Model 7: beta	-1237.774059
Model 8: beta&w>1	-1237.774377


Model 0 vs 1	0.017014000000017404

Model 2 vs 1	0.017014000000017404

Model 8 vs 7	6.359999997584964E-4