TreeTools
Create, Modify and Analyse Phylogenetic Trees
Last update: 19 August 2023
Software version identifier: 1.9.1, 1.9.2, 0.1.2, 0.1.3, 0.1.4, 1.0.0, 1.1.0, 1.2.0, 1.3.0, 1.3.1, 1.4.0, 1.4.1, 1.4.2, 1.4.3, 1.4.4, 1.4.5, 1.5.0, 1.5.1, 1.6.0, 1.7.0, 1.7.1, 1.7.2, 1.7.3, 1.8.0, 1.9.0, 1.10.0
Copyright license: GNU General Public License
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 <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
- Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix
- Phylogenetic Signal and Bias in Paleontology
- A new balance index for phylogenetic trees
- Nexus: An Extensible File Format for Systematic Information
