Create, Modify and Analyse Phylogenetic Trees

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2021) , and of tree balance (Mir et al. 2013) ; artificial extinction (Asher & Smith, 2021) ; import and export of trees from Newick, Nexus (Maddison et al. 1997) , and TNT <> formats; and analysis of splits and cladistic information.


Reference manual

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1.5.1 by Martin R. Smith, 13 days ago,

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Authors: Martin R. Smith [aut, cre, cph] , Emmanuel Paradis [cph]

Documentation:   PDF Manual  

GPL (>= 3) license

Imports bit64, colorspace, fastmatch, phangorn, R.cache, Rdpack

Depends on ape

Suggests knitr, Rcpp, rmarkdown, shiny, testthat, vdiffr

Linking to Rcpp

System requirements: C++14

Imported by Quartet, Rogue, TBRDist, TotalCopheneticIndex, TreeDist, TreeSearch.

See at CRAN