Understand Tracer parameters

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GretaRom

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Jan 30, 2024, 12:21:58 PMJan 30
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Dear all,

Could you help me with ESS problem?
I used Beast 1.10.4 to analyze 100 Echovirus sequences. 
I am new to phylogenetic analysis but I read all beast tutorials. However I still don't understand which parameters must have ESS>200 and which should have ESS>200.
Here you can see my runs. The sequences were analyzed with GTR+G+I (derived from MEGA): 
-10^8 chain and log every 10^4 with uncorrelated lognormal relaxed clock  and coalescent costant tree prior (96.log)
-10^8 chain and log every 10^4 with strict clock and coalescent constant tree prior (parsedStrict.log)

So, some parameters are good and others not at all. 
1)Can you explain to me which run should I consider valid and which parameters should I consider as essential for ESS value (also for future analysis)?
2)Should I run again the analysis using a longer chain?
3) What is the Burn-in parameter and why is so important?
4) Do you think that my molecular clock setting are suitable?

THANK YOU SO MUCH
Greta

PS: If you have books or article to better understand these parameters will help. Thank youStrictEstimates.pngStrictTrace.pngUncorrelatedEstimats.pngUncorrelatedTrace.png 




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