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 
[aut, cre, cph],
Martin Brazeau
[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:
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-devel (arm64): TreeSearch_1.5.1.tgz, r-release (arm64): TreeSearch_1.5.1.tgz, r-oldrel (arm64): TreeSearch_1.5.1.tgz, r-devel (x86_64): 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.