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) doi:10.1016/j.mbs.2012.10.005; 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 formats; and analysis of splits and cladistic information.