Title: Create, Modify and Analyse Phylogenetic Trees
phangorn by Klaus Scheip <doi:10.1093/bioinformatics/btq706>
Description: Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include: generation of trees with specified shapes;
rooting of trees and extraction of subtrees;
calculation and depiction of node support;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
analysis of partitions and partition information.
Imports: colorspace, phangorn (>= 2.2.1), R.cache
Suggests: knitr, Rcpp, Rdpack, rmarkdown, shiny, testthat

analysis of partitions and cladistic information.
Imports: bit64, colorspace, phangorn (>= 2.2.1), R.cache

generation of trees with specified shapes;
and analysis of splits and cladistic information.

Copyright: Incorporates C/C++ code from 'ape' by Emmanuel Paradis
Imports: bit64, colorspace, phangorn (>= 2.2.1), R.cache, Rdpack
Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, vdiffr

person("Martin R.", 'Smith', role = c("aut", "cre", "cph"),
person(given = "Emmanuel", family = "Paradis", role = c("cph"),

Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, vdiffr (>= 1.0.0)

calculation and depiction of split support;
of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>,
artificial extinction (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>;
Imports: bit64, colorspace, fastmatch, phangorn (>= 2.2.1), R.cache,
Suggests: knitr, Rcpp, rmarkdown, shiny, testthat (>= 3.0), vdiffr (>=

Imports: bit64, colorspace, fastmatch (>= 1.1.3), phangorn (>= 2.2.1),

plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
Imports: bit64, lifecycle, colorspace, fastmatch (>= 1.1.3), R.cache,
Suggests: spelling, knitr, phangorn (>= 2.2.1), Rcpp, rmarkdown, shiny,

artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
Imports: bit64, lifecycle, colorspace, fastmatch (>= 1.1.3), methods,
Suggests: spelling, knitr, phangorn (>= 2.2.1), Rcpp (>= 1.0.8),
rmarkdown, shiny, testthat (>= 3.0), vdiffr (>= 1.0.0),