Question: How do I interpret results from the Tracer while doing phylogenetic analysis by bayesian method ?
0
gravatar for lokraj2003
22 months ago by
lokraj200380
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
CP1.mu 0.76 CP2.mu 1.221
CP3.mu 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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 937 users visited in the last hour