Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith, 2020) ; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) , including the Nye et al. (2006) metric ; the Matching Split Distance (Bogdanowicz & Giaro 2012) ; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance , and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) . Includes tools for visualizing the landscape of a tree space, and for calculating the median of a set of trees under any distance metric.


Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


2.0.3 by Martin R. Smith, 3 months ago

https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist/

Report a bug at https://github.com/ms609/TreeDist/issues/

Browse source code at https://github.com/cran/TreeDist

Authors: Martin R. Smith [aut, cre, cph, prg] , Roy Jonker [prg, cph] , Yong Yang [ctb, cph] , Yi Cao [ctb, cph]

Documentation:   PDF Manual  

GPL (>= 3) license

Imports ape, colorspace, memoise, phangorn, Rdpack, shiny, shinyjs, TreeTools

Depends on stats

Suggests bookdown, cluster, kdensity, knitr, MASS, protoclust, Quartet, readxl, rmarkdown, Rcpp, rgl, testthat, Ternary, TreeDistData, TreeSearch, vdiffr, viridisLite

Linking to Rcpp, TreeTools

System requirements: C++14

Imported by TBRDist.

See at CRAN