TreeTools

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) [doi:10.1371/journal.pone.0212942]; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) [doi:10.1093/sysbio/syab072], and of tree balance (Mir et al. 2013, Lemant et al. 2022) [doi:10.1016/j.mbs.2012.10.005], [doi:10.1093/sysbio/syac027]; artificial extinction (Asher & Smith, 2022) [doi:10.1093/sysbio/syab072]; import and export of trees from Newick, Nexus (Maddison et al. 1997) [doi:10.1093/sysbio/46.4.590], and TNT [https://www.lillo.org.ar/phylogeny/tnt/] formats; and analysis of splits and cladistic information.

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