TreeSearch
Phylogenetic Analysis with Discrete Character Data
Last update: 26 August 2023
Software version identifier: 1.3.1, 1.3.2, 0.0.6, 0.0.8, 0.1.0, 0.1.2, 0.2.0, 0.2.1, 0.2.2, 0.3.0, 0.3.2, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 1.0.0, 1.0.1, 1.1.0, 1.1.1, 1.1.2, 1.2.0, 1.3.0, 1.4.0
Copyright license: GNU General Public License
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.
- An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data
- Using Information Theory to Detect Rogue Taxa and Improve Consensus Trees
- Robust Analysis of Phylogenetic Tree Space
- A Successive Approximations Approach to Character Weighting
- Towards an Inclusive Philosophy for Phylogenetic Inference
