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Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model

Fig 1

Branch rate parameterisations.

Top left: the prior density of a branch rate r under a Log-normal(−0.5σ², σ) distribution (with its mean fixed at 1). The function for transforming into branch rates is depicted for real (top right), cat (bottom left), and quant (bottom right). For visualisation purposes, there are only 10 bins/pieces displayed, however in practice we use 2N − 2 bins for cat and 100 pieces for quant. The first and final quant pieces are equal to the underlying function (solid lines) however the pieces in between use linear approximations of this function (dashed lines).

doi: https://doi.org/10.1371/journal.pcbi.1008322.g001