My best substitution model was estimated to be GTR+G+I using JmodelTest.
in Beauti setting, all given values (including gamma shape,proportion of invariant and rate ac,ag etc) was set and frequencies was set as empirical. (all parameters in site model were set estimate except Proportion invariant and rate CT remained as default-unticked)
i have run MCMC chain length from 1million to 30 million and the ESS values for posterior, prior and rate CG still below 200.
May i know how can i improve the ESS value?
Hi Artur,
here i attached my Nexus file for your reference.
and one of the xml file and log file i got after running beast.
and also a screenshot for your quick glance.
Thanks.
Hi Chen, im now trying running 40 million ngen. Thx.
Hi Artur, if increasing the scale factor in most parameters in my operators tab to increase ESS, will that have an effect on my phylogenetic analysis?
Hi Maccus Hao Jie Wong,
If the number of your data is high (e.g., more than 50 accessions), you must run more than 50 million generations since the data will converge each other (I mean when you obtain the same or almost the same result of each marker).
Please run each marker once (however, it is better to run twice and then combine the logs) and then combine your data using logCombiner in order to see the final result.
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