Reference Guide

• Tree (main class)
  • Tree
  • TreeError
• Tree operations
  • Walker
  • add_branch_values()
  • add_leaf_names()
  • assert_root_consistency()
  • closest_descendant_leaf()
  • closest_leaf()
  • closest_relative_leaf()
  • common_ancestor()
  • create_dichotomic_sister()
  • distance_matrix()
  • evolutionary_distinctness()
  • farthest_descendant()
  • farthest_nodes()
  • get_common_values()
  • get_distance_fn()
  • insert_intermediate()
  • interchange_references()
  • join_branch()
  • ladderize()
  • leaves_vs_random()
  • make_name()
  • make_partitions()
  • mean_distance()
  • midpoint()
  • move()
  • nearest_taxon_index()
  • net_relatedness_index()
  • partition_id()
  • phylogenetic_diversity()
  • populate()
  • populate_uniform()
  • populate_yule()
  • rehang()
  • remove()
  • resolve_polytomy()
  • robinson_foulds()
  • root_at()
  • set_midpoint_outgroup()
  • set_outgroup()
  • sort()
  • swap_props()
  • to_dendrogram()
  • to_ultrametric()
  • traverse()
  • traverse_bfs()
  • traverse_full()
  • unroot()
  • update_size()
  • update_sizes_all()
  • update_sizes_from()
  • walk()
• Parsers
  • Newick
  • Nexus
• Phylogenetic trees
  • PhyloTree
  • EvolEvent
• Multiple Sequence Alignments (SeqGroup)
  • SeqGroup
• Taxonomy databases
  • NCBITaxa
  • GTDBTaxa
• Smartview (web graphics)
  • Smartview
  • Explorer
  • Layout
  • Faces
  • Graphics
  • Coordinates
  • Draw
• Treeview (qt graphics)
  • TreeStyle
  • NodeStyle
  • Faces
• Tree matcher
  • TreePattern
  • match()
  • search()