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.

Package details

AuthorMartin R. Smith [aut, cre, cph] (<>), Martin Brazeau [cph] (<>)
MaintainerMartin R. Smith <>
LicenseGPL (>= 3)
URL (doc) (devel)
Package repositoryView on CRAN
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TreeSearch documentation built on May 29, 2024, 8:19 a.m.