TreeSearch: Phylogenetic Tree Search Using Custom Optimality Criteria

Search for phylogenetic trees that are optimal using a user-defined criterion. 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. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> using the "Morphy" library. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.

Version: 1.0.1
Depends: R (≥ 3.5.0)
Imports: ape (≥ 5.1.2), cli (≥ 3.0), cluster, fastmatch (≥ 1.1.3), future, phangorn (≥ 2.2.1), promises, protoclust, Rcpp, Rdpack (≥ 0.7), Rogue (> 1.0.0), shiny, shinyjs, stats, TreeDist (> 2.0.3), TreeTools (≥ 1.5.0)
LinkingTo: Rcpp, TreeTools
Suggests: knitr, rmarkdown, Quartet, testthat, vdiffr (≥ 1.0.0)
Published: 2021-09-27
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/, https://github.com/ms609/TreeSearch/
NeedsCompilation: yes
SystemRequirements: C++14
Language: en-GB
Citation: TreeSearch citation info
Materials: NEWS
CRAN checks: TreeSearch results

Documentation:

Reference manual: TreeSearch.pdf
Vignettes: Tree search with custom optimality criteria
Getting started: Installing R and TreeSearch
Calculating concavity profiles for profile parsimony
Tree Search with Profile Parsimony
Getting started: Simple tree searches

Downloads:

Package source: TreeSearch_1.0.1.tar.gz
Windows binaries: r-devel: TreeSearch_1.0.1.zip, r-devel-UCRT: TreeSearch_1.0.1.zip, r-release: TreeSearch_1.0.1.zip, r-oldrel: TreeSearch_1.0.1.zip
macOS binaries: r-release (arm64): TreeSearch_1.0.1.tgz, r-release (x86_64): TreeSearch_1.0.1.tgz, r-oldrel: TreeSearch_1.0.1.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.