Calibration points not taking effect in MCMCTree (PAML 4.9)
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guo
Dec 18, 2025, 8:49:46 PM (6 hours ago) Dec 18
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Hi Kostas,
I hope you are doing well.
I am writing to ask for your advice regarding a calibration issue I encountered when running MCMCTree in PAML version 4.9.
In my analysis, I specified two calibration points in the tree file (as shown in the attached tree), and the MCMC run completed successfully. However, when I visualized the resulting output tree (.tre) in FigTree, it appears that the calibration constraints were not reflected in the divergence time estimates, as if the calibrations did not take effect.
Thank you very much for your time and help.
Best regards
I hope you are doing well.
I am writing to ask for your advice regarding a calibration issue I encountered when running MCMCTree in PAML version 4.9.
In my analysis, I specified two calibration points in the tree file (as shown in the attached tree), and the MCMC run completed successfully. However, when I visualized the resulting output tree (.tre) in FigTree, it appears that the calibration constraints were not reflected in the divergence time estimates, as if the calibrations did not take effect.
Thank you very much for your time and help.
Best regards
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