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) . Calculates the median of a set of trees under any distance metric.


Reference manual

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1.2.1 by Martin R. Smith, a month 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, TreeTools

Depends on stats

Suggests bookdown, cluster, kdensity, knitr, MASS, Quartet, rmarkdown, Rcpp, testthat, Ternary, TreeDistData, TreeSearch, vdiffr

Linking to Rcpp

System requirements: C++11

Imported by TBRDist.

See at CRAN