TreeSearch: Phylogenetic Analysis with Discrete Character Data

Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.

Version: 1.5.1
Depends: R (≥ 3.5.0)
Imports: ape (≥ 5.6), cli (≥ 3.0), cluster, fastmatch (≥ 1.1.3), fs, future, PlotTools, promises, protoclust, Rcpp, Rdpack (≥ 0.7), Rogue (> 2.0.0), shiny (≥ 1.6.0), shinyjs, stats, TreeDist (≥ 2.6.3), TreeTools (≥ 1.10.0)
LinkingTo: Rcpp, TreeTools
Suggests: knitr, phangorn (≥ 2.2.1), Quartet, readxl, rmarkdown, shinytest, spelling, testthat, vdiffr (≥ 1.0.0)
Published: 2024-05-23
DOI: 10.32614/CRAN.package.TreeSearch
Author: Martin R. Smith ORCID iD [aut, cre, cph], Martin Brazeau ORCID iD [cph]
Maintainer: Martin R. Smith <martin.smith at>
License: GPL (≥ 3)
Copyright: Incorporates C/C++ code from Morphy Phylogenetic Library by Martin Brazeau <> (GPL3)
URL: (doc), (devel)
NeedsCompilation: yes
SystemRequirements: C++17
Language: en-GB
Citation: TreeSearch citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: TreeSearch results


Reference manual: TreeSearch.pdf
Vignettes: Tree search with custom optimality criteria
Getting started: Installing R and TreeSearch
Profile parsimony
Tree search with Profile parsimony
Getting started: Simple tree searches
Getting started: Exploring tree space


Package source: TreeSearch_1.5.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): TreeSearch_1.5.1.tgz, r-oldrel (arm64): TreeSearch_1.5.1.tgz, r-release (x86_64): TreeSearch_1.5.1.tgz, r-oldrel (x86_64): TreeSearch_1.5.1.tgz
Old sources: TreeSearch archive

Reverse dependencies:

Reverse suggests: CongreveLamsdell2016, TreeDist


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