Index A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U | W | Λ A add() (bdms.utils.RandomizedSet method) add_child() (bdms.tree.TreeNode method) add_face() (bdms.tree.TreeNode method) add_feature() (bdms.tree.TreeNode method) add_features() (bdms.tree.TreeNode method) add_note() (bdms.tree.TreeError method) add_sister() (bdms.tree.TreeNode method) B bdms module bdms.mutators module bdms.poisson module bdms.tree module bdms.utils module C check_monophyly() (bdms.tree.TreeNode method) choice() (bdms.utils.RandomizedSet method) compare() (bdms.tree.TreeNode method) ConstantProcess (class in bdms.poisson) convert_to_ultrametric() (bdms.tree.TreeNode method) cophenetic_matrix() (bdms.tree.TreeNode method) copy() (bdms.tree.TreeNode method) D del_feature() (bdms.tree.TreeNode method) delete() (bdms.tree.TreeNode method) describe() (bdms.tree.TreeNode method) detach() (bdms.tree.TreeNode method) DiscreteMutator (class in bdms.mutators) DiscreteProcess (class in bdms.poisson) E event (bdms.tree.TreeNode attribute) evolve() (bdms.tree.TreeNode method) expand_polytomies() (bdms.tree.TreeNode method) F from_parent_child_table() (bdms.tree.TreeNode static method) from_skbio() (bdms.tree.TreeNode static method) G GaussianMutator (class in bdms.mutators) get_ancestors() (bdms.tree.TreeNode method) get_ascii() (bdms.tree.TreeNode method) get_cached_content() (bdms.tree.TreeNode method) get_children() (bdms.tree.TreeNode method) get_closest_leaf() (bdms.tree.TreeNode method) get_common_ancestor() (bdms.tree.TreeNode method) get_descendants() (bdms.tree.TreeNode method) get_distance() (bdms.tree.TreeNode method) get_edges() (bdms.tree.TreeNode method) get_farthest_leaf() (bdms.tree.TreeNode method) get_farthest_node() (bdms.tree.TreeNode method) get_leaf_names() (bdms.tree.TreeNode method) get_leaves() (bdms.tree.TreeNode method) get_leaves_by_name() (bdms.tree.TreeNode method) get_midpoint_outgroup() (bdms.tree.TreeNode method) get_monophyletic() (bdms.tree.TreeNode method) get_sisters() (bdms.tree.TreeNode method) get_topology_id() (bdms.tree.TreeNode method) get_tree_root() (bdms.tree.TreeNode method) H HomogeneousProcess (class in bdms.poisson) I InhomogeneousProcess (class in bdms.poisson) is_leaf() (bdms.tree.TreeNode method) is_root() (bdms.tree.TreeNode method) iter_ancestors() (bdms.tree.TreeNode method) iter_descendants() (bdms.tree.TreeNode method) iter_edges() (bdms.tree.TreeNode method) iter_leaf_names() (bdms.tree.TreeNode method) iter_leaves() (bdms.tree.TreeNode method) iter_prepostorder() (bdms.tree.TreeNode method) iter_search_nodes() (bdms.tree.TreeNode method) K KdeMutator (class in bdms.mutators) L ladderize() (bdms.tree.TreeNode method) M module bdms bdms.mutators bdms.poisson bdms.tree bdms.utils mutate() (bdms.mutators.DiscreteMutator method) (bdms.mutators.GaussianMutator method) (bdms.mutators.KdeMutator method) (bdms.mutators.Mutator method) Mutator (class in bdms.mutators) N n_mutations (bdms.tree.TreeNode attribute) P populate() (bdms.tree.TreeNode method) prob() (bdms.mutators.DiscreteMutator method) (bdms.mutators.GaussianMutator method) (bdms.mutators.KdeMutator method) (bdms.mutators.Mutator method) Process (class in bdms.poisson) prune() (bdms.tree.TreeNode method) prune_unsampled() (bdms.tree.TreeNode method) R RandomizedSet (class in bdms.utils) remove() (bdms.utils.RandomizedSet method) remove_child() (bdms.tree.TreeNode method) remove_mutation_events() (bdms.tree.TreeNode method) remove_sister() (bdms.tree.TreeNode method) render() (bdms.tree.TreeNode method) resolve_polytomy() (bdms.tree.TreeNode method) robinson_foulds() (bdms.tree.TreeNode method) S sample_survivors() (bdms.tree.TreeNode method) search_nodes() (bdms.tree.TreeNode method) set_outgroup() (bdms.tree.TreeNode method) set_style() (bdms.tree.TreeNode method) show() (bdms.tree.TreeNode method) slice() (bdms.tree.TreeNode method) sort_descendants() (bdms.tree.TreeNode method) standardize() (bdms.tree.TreeNode method) state_attr (bdms.tree.TreeNode attribute) state_space (bdms.mutators.DiscreteMutator attribute) swap_children() (bdms.tree.TreeNode method) T t (bdms.tree.TreeNode attribute) traverse() (bdms.tree.TreeNode method) Tree (in module bdms) TreeError TreeNode (class in bdms.tree) (in module bdms) U unroot() (bdms.tree.TreeNode method) W waiting_time_rv() (bdms.poisson.ConstantProcess method) (bdms.poisson.DiscreteProcess method) (bdms.poisson.HomogeneousProcess method) (bdms.poisson.InhomogeneousProcess method) (bdms.poisson.Process method) with_traceback() (bdms.tree.TreeError method) write() (bdms.tree.TreeNode method) Λ Λ() (bdms.poisson.ConstantProcess method) λ() (bdms.poisson.ConstantProcess method) Λ() (bdms.poisson.DiscreteProcess method) λ() (bdms.poisson.DiscreteProcess method) Λ() (bdms.poisson.HomogeneousProcess method) λ() (bdms.poisson.HomogeneousProcess method) Λ() (bdms.poisson.InhomogeneousProcess method) λ() (bdms.poisson.InhomogeneousProcess method) Λ() (bdms.poisson.Process method) λ() (bdms.poisson.Process method) λ_homogeneous() (bdms.poisson.ConstantProcess method) (bdms.poisson.DiscreteProcess method) (bdms.poisson.HomogeneousProcess method) λ_inhomogeneous() (bdms.poisson.InhomogeneousProcess method) Λ_inv() (bdms.poisson.ConstantProcess method) (bdms.poisson.DiscreteProcess method) (bdms.poisson.HomogeneousProcess method) (bdms.poisson.InhomogeneousProcess method) (bdms.poisson.Process method)