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.">

TreeSearch: Phylogenetic Analysis with Discrete Character Data (original) (raw)

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: 1.7.0
Depends: R (≥ 4.0)
Imports: ape (≥ 5.6), cli (≥ 3.0), cluster, fastmap, fastmatch (≥ 1.1.3), fs, future, PlotTools, promises, protoclust, Rcpp, Rdpack (≥ 0.7), Rogue (> 2.0.0), shiny (≥ 1.6.0), shinyjs, stats, stringi, TreeDist (≥ 2.6.3), TreeTools (≥ 1.16)
LinkingTo: Rcpp, TreeTools
Suggests: knitr, phangorn (≥ 2.2.1), Quartet, readxl, rmarkdown, shinytest, spelling, testthat, vdiffr (≥ 1.0.0)
Published: 2025-08-23
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

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