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