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 [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 byMartin 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: | Paleontology,Phylogenetics |
| CRAN checks: | TreeSearch results |