Phylogenetic Analysis with Discrete Character Data R package TreeSearch version 1.7.0 CRAN Task View: Paleontology (https://CRAN.R-project.org/view=Paleontology) CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) 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. Software 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), Martin R. Smith <martin.smith@durham.ac.uk> Comprehensive R Archive Network (CRAN) Martin R. Smith [aut, cre, cph] (ORCID: <https://orcid.org/0000-0001-5660-1727>), Martin Brazeau [cph] (ORCID: <https://orcid.org/0000-0002-0650-1282>) GPL (>= 3) 2025-08-23 application/tgz https://CRAN.R-project.org/package=TreeSearch doi:10.32614/CRAN.package.TreeSearch en-GB