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

Fig 12

Round 4: Benchmarking the NER operators.

Top: the learned weights (left) behind the two NER operators (NER{} and ), and the relative difference between their acceptance rates α (right), are presented as functions of sequence length. Logistic and logarithmic regression models are shown, respectively. Bottom: maximum clade credibility tree of the bony fish dataset by Broughton et al. 2013 [53]. This alignment received the strongest boost from NER, likely due to its high topological uncertainty and branch rate variance. Branches are coloured by substitution rate, the y-axis shows time units, and internal nodes are labelled with posterior clade support. Tree visualised using UglyTrees [59].

doi: https://doi.org/10.1371/journal.pcbi.1008322.g012