TreeSearch

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.