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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1.0.0 by Martin R. Smith, 7 days 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, TreeTools

Depends on stats

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

Linking to Rcpp

Imported by TBRDist.

See at CRAN