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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 durham.ac.uk>
BugReports: https://github.com/ms609/TreeSearch/issues/
License: GPL (≥ 3)
Copyright: Incorporates C/C++ code from Morphy Phylogenetic Library by Martin Brazeau <https://github.com/mbrazeau/MorphyLib> (GPL3)
URL: https://ms609.github.io/TreeSearch/ (doc), https://github.com/ms609/TreeSearch/ (devel)
NeedsCompilation: yes
SystemRequirements: C++17
Language: en-GB
Citation: TreeSearch citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: TreeSearch results

Documentation:

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

Downloads:

Package source: TreeSearch_1.5.1.tar.gz
Windows binaries: r-devel: TreeSearch_1.5.1.zip, r-release: TreeSearch_1.5.1.zip, r-oldrel: TreeSearch_1.5.1.zip
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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=TreeSearch to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.