Bio::Phylo API methods for Tree

From Evolutionary Informatics Working Group
Revision as of 10:18, 10 March 2009 by Vgopalan (talk) (Bio::Phylo methods for Tree manipulation)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Bio::Phylo API methods for phylogenetic trees

--vivek 10:18, 10 March 2009 (EDT)

The multiple trees are handled in the Forest class. Forest ==> Tree ==> Node

Class: Forest - Container of multiple trees

  • inserts(trees) - inserts tree
  • get_default_tree()
  • check_taxa() - Validates the taxon links of nodes in the tree
  • to_newick()
  • make_taxa()
  • to_nexus()
  • Inherited ListAble class
  • add_set()
  • clear()
  • clone()
  • contains()
  • first()
  • get_by_name()
  • get_by_regular_expression()
  • get_by_values()
  • get_entities()


Class: Tree

  • set_as_default()
  • set_not_default()
  • get_terminals()
  • get_internals()
  • get_root()
  • get_tallest_tip()
  • get_mrca()
  • is_rooted()
  • is_binary()
  • is_ultrametric()
  • is_monophyletic(tip_nodes,node)
  • is_paraphyletic(nodes,node)
  • calc_symdiff(other_tree) - calculates symmetric difference
  • calc_fp() - calculates fair proposition value for each terminal
  • calc_shapely - calculates shapely value for each terminal
  • visit_depth_first()
  • visit_breadth_first()
  • visit_level_order()
  • ultrametrize()
  • scale(value)
  • resolve()
  • prune_tips()
  • keep_tips()
  • negative_to_zero()
  • exponentiate()
  • log_transformation()
  • remove_unbranched_internal()
  • to_newick()
  • to_xml()
  • to_svg()
  • to_json()

Class: Node

  • new()
  • prune_child()
  • collapse_node()
  • set_parent()
  • set_first_daughter()
  • set_last_daugther()
  • set_previous_sister()
  • set_next_sister()
  • set_child()
  • set_branch_length()
  • set_node_below()
  • set_tree()


  • get_parent()
  • get_first_daughter()
  • get_last_daughter()
  • get_previous_sister()
  • get_next_sister()
  • get_branch_length()
  • get_ancestors()
  • get_sisters()
  • get_children()
  • get_child()
  • get_descendents()
  • get_terminals()
  • get_internals()
  • get_mrca()
  • get_left_most_terminal()
  • get_right_most_terminal()
  • get_tree()


  • is_terminal()
  • is_internal()
  • is_first()
  • is_last();
  • is_root()
  • is_descendent_of()
  • is_ancestor_of()
  • is_sister_of()
  • is_child_of()
  • is_outgroup_of()
  • can_contain()
  • calc_path_to_root()
  • calc_nodes_to_root()
  • calc_max_nodes_to_tips()
  • calc_min_nodes_to_tips()
  • calc_max_path_to_tips()
  • calc_min_path_to_tips()
  • calc_patristic_distance()
  • calc_nodal_distance()
  • visit_depth_first()
  • visit_breadth_first()
  • visit_level_order()
  • to_json()
  • to_xml()
  • to_newick()