Low GTR rate ESS

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Jyotishko Koley

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Apr 19, 2025, 2:07:46 PM4/19/25

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Hello all,

I am running a 16S alignment with 190 sequences, and I ran 6 independent runs: 2 with 35 million chain length and 4 with 60 million. All of my ESS values are high except for the 6 rate parameters (rateAC, rateAG, etc.). In my outputted MCC tree, the posterior probabilities were very variable, with many over 0.9 but several below 0.1. Are the low rate ESSs contributing to this? And if so, what can I do to improve them?

Thanks

Artem B

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Apr 22, 2025, 2:33:22 AM4/22/25

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Hi Jyotishko,

Checking the MCMC traces of the rates makes sense. Can you provide a screenshot?

Cheers,
Artem

воскресенье, 20 апреля 2025 г. в 02:07:46 UTC+8, Jyotishko Koley:

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