Question: How do I interpret results from the Tracer while doing phylogenetic analysis by bayesian method ?
gravatar for lokraj2003
22 months ago by
lokraj200380 wrote:

I am doing phylodynamic analysis of virus sequences using bayesian method using BEAUti and BEAST. As a part of my analysis I am using Tracer to check how my model is working.

I can interpret some of the results like from the Tracer like :

clock.rate - rate of nucleotide substitution

treemodel.rootheight- time when divergence occured

ESS- measures sampling quality (ideally has to be greater that 200)

But there are other many terms on this analysis which I have no idea how to explain.

Please can anybody help me to find out what other aspects of the evolution can be explained using this table.

posterior -33531.076
prior -481.982
likelihood -33049.094
treeModel.rootHeight 32.271
tmrca(Brazil) 3.853
tmrca(Canada) 16.644
tmrca(China ) 11.752
tmrca(Columbia) 1
tmrca(Thailand) 1.093
tmrca(USA) 32.271
tmrca(allseq) 32.271 < constant.popSize 43.595
CP1.kappa 18.716
CP2.kappa 17.16
CP3.kappa 22.796
frequencies1 0.224
frequencies3 0.221
frequencies4 0.26 5001 0.76 1.221 1.019
clock.rate 1.354E-3
meanRate 1.354E-3
CP1.treeLikelihood -9462.258
CP2.treeLikelihood -12520.305
branchRates 0E0 coalescent -467.376

beast alignment bayesian tracer • 568 views
ADD COMMENTlink modified 10 weeks ago by Biostar ♦♦ 20 • written 22 months ago by lokraj200380
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