ape (>= 5.0), cli (>= 3.0), colorspace, memoise, phangorn (>=
2.2.1), Rdpack (>= 0.7), shiny, shinyjs, TreeTools (>= 1.5.0)
bookdown, cluster, ggplot2, kdensity, knitr, MASS, parallel,
protoclust, Quartet, readxl, rmarkdown, Rcpp, rgl, testthat (>=
3.0), Ternary (>= 1.1.2), TreeDistData (> 0.1.0), TreeSearch,
Umatrix, vdiffr (>= 1.0.0)

Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.
bookdown, cluster, ggplot2, hypervolume, kdensity, knitr,
MASS, parallel, protoclust, Quartet, readxl, rmarkdown, Rcpp,
rgl, spelling, testthat (>= 3.0), Ternary (>= 1.1.2),
TreeDistData (> 0.1.0), TreeSearch, Umatrix, uwot, vdiffr (>=
1.0.0)

Jonker-Volgenant Linear Assignment Problem implementation by
Roy Jonker modified by Yong Yang and Yi Cao.
ape (>= 5.0), cli (>= 3.0), colorspace, memoise, phangorn (>=
2.2.1), Rdpack (>= 0.7), shiny, shinyjs, TreeTools (>= 1.7.0),
bookdown, cluster, ggplot2, hypervolume, kdensity, knitr,
MASS, parallel, protoclust, Quartet, readxl, rmarkdown, Rcpp
(>= 1.0.8), rgl, spelling, testthat (>= 3.0), Ternary (>=
1.1.2), TreeDistData (> 0.1.0), TreeSearch, Umatrix, uwot,
vdiffr (>= 1.0.0),

ape (>= 5.0), cli (>= 3.0), colorspace, memoise, phangorn (>=
2.2.1), Rdpack (>= 0.7), shiny, shinyjs, TreeTools (>=
1.7.1.9000),
bookdown, cluster, ggplot2, hypervolume, kdensity, knitr,
MASS, parallel, protoclust, Quartet, readxl, rmarkdown, Rcpp
(>= 1.0.8), rgl, Rogue, spelling, testthat (>= 3.0), Ternary
(>= 1.1.2), TreeDistData (> 0.1.0), TreeSearch, Umatrix, uwot,
vdiffr (>= 1.0.0),