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XML specification

Rate shift times for Skyline model

How to specify rate shift times in BDSKY

Analysing fully extinct clades

To analyse fully extinct clades using FBD model, one needs to specify offsets. See https://taming-the-beast.org/tutorials/FBD-tutorial/ section 5 for more details.

Citation for the offset implementation: Barido-Sottani, J., van Tiel, N. M. A., Hopkins, M. J., Wright, D. F., Stadler, T., & Warnock, R. C. M. (2020). Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference. Frontiers in Ecology and Evolution, 8, 183. https://doi.org/10.3389/fevo.2020.00183