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 |