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TreeSearch: Phylogenetic Analysis with Discrete Character 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.
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Package details |
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| Author | Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>) |
| Maintainer | Martin R. Smith <martin.smith@durham.ac.uk> |
| License | GPL (>= 3) |
| Version | 1.6.0 |
| URL | https://ms609.github.io/TreeSearch/ (doc) https://github.com/ms609/TreeSearch/ (devel) |
| Package repository | View on CRAN |
| Installation |
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