Maximum Likelihood Inference on Multi-State Trees

Inference of a multi-states birth-death model from a phylogeny, comprising a number of states N, birth and death rates for each state and on which edges each state appears. Inference is done using a hybrid approach: states are progressively added in a greedy approach. For a fixed number of states N the best model is selected via maximum likelihood. Reference: J. Barido-Sottani and T. Stadler (2017) .


Version 1.1.1

  • Modified examples to use fixed trees instead of randomly generated ones (for compatibility with future R releases)

Version 1.1.0

  • Fixed bug that could lead to incorrect likelihood calculation when using trees with collapsed clades
  • Removed invalid real time mode option from ML inference
  • Added vignette to the documentation

Reference manual

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1.2.0 by Joelle Barido-Sottani, a year ago

Browse source code at

Authors: Joelle Barido-Sottani [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports ape, foreach

Suggests knitr, doParallel

See at CRAN