TreeSearch: Phylogenetic Analysis with Morphological 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: 1.1.1
Depends: R (≥ 3.5.0)
Imports: ape (≥ 5.6), cli (≥ 3.0), cluster, fastmatch (≥ 1.1.3), future, promises, protoclust, Rcpp, Rdpack (≥ 0.7), Rogue (> 2.0.0), shiny (≥ 1.6.0), shinyjs, stats, TreeDist (≥ 2.3.0), TreeTools (≥ 1.7.0)
LinkingTo: Rcpp, TreeTools
Suggests: knitr, phangorn (≥ 2.2.1), Quartet, rmarkdown, shinytest, spelling, testthat, vdiffr (≥ 1.0.0)
Published: 2022-03-22
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
Profile parsimony
Tree Search with Profile Parsimony
Getting started: Simple tree searches

Downloads:

Package source: TreeSearch_1.1.1.tar.gz
Windows binaries: r-devel: TreeSearch_1.1.1.zip, r-release: TreeSearch_1.1.1.zip, r-oldrel: TreeSearch_1.1.1.zip
macOS binaries: r-release (arm64): TreeSearch_1.1.1.tgz, r-release (x86_64): TreeSearch_1.1.1.tgz, r-oldrel: TreeSearch_1.1.1.tgz
Old sources: TreeSearch archive

Reverse dependencies:

Reverse suggests: CongreveLamsdell2016, TreeDist

Linking:

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