Nested Phylogenetic Tree Simulator

Simulates nested phylogenetic trees (gene trees in species tree, symbiont trees in host trees) using birth-death processes and transfers between lineages. Simulations of gene trees within species trees are performed using a three-tree model with species trees, locus trees, and gene trees. The cophylogenetic birth-death process is used to simulate sets of host and symbiont trees with extant associations between tips. For more information about the three-tree model see: Mallo et al. (2015) , Rasmussen and Kellis (2012) .


Reference manual

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1.1.0 by Wade Dismukes, 8 months ago

Browse source code at

Authors: Wade Dismukes [aut, cre] , Tracy A. Heath [aut] , Josh Justison [ctb] , Damien de Vienne [ctb] , Liam Revell [ctb] , Emmanuel Paradis [ctb] , Klaus Schliep [ctb] , Ben Bolker [ctb] , Luke J. Harmon [ctb] , Joseph W. Brown [ctb]

Documentation:   PDF Manual  

GPL-3 license

Imports Rcpp, apTreeshape, graphics, methods

Depends on ape

Suggests knitr, rmarkdown, testthat

Linking to Rcpp, RcppArmadillo

System requirements: C++11

See at CRAN