tree/bipartition/functions.hpp File Reference

#include "genesis/tree/tree.hpp"
#include "genesis/tree/bipartition/bipartition.hpp"
#include "genesis/utils/math/bitvector.hpp"
#include <string>
#include <vector>

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Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::tree

Functions
std::vector< Bipartition >	bipartition_set (Tree const &tree)
std::vector< size_t >	find_monophyletic_subtree_edges (Tree const &tree, std::vector< Bipartition > const &bipartitions, std::vector< TreeNode const * > const &nodes, bool include_splitting_edges=true, bool include_leaf_edges=true)
	Find clades of the tree that are monophyletic with respect to the given list of nodes, that is, clades that only contain nodes from that list. Return all edge indices of those clades. More...
std::vector< size_t >	find_monophyletic_subtree_edges (Tree const &tree, std::vector< std::string > const &node_names, bool include_splitting_edges, bool include_leaf_edges)
std::vector< size_t >	find_monophyletic_subtree_edges (Tree const &tree, std::vector< TreeNode const * > const &nodes, bool include_splitting_edges, bool include_leaf_edges)
Bipartition	find_smallest_subtree (Tree const &tree, std::vector< Bipartition > const &bipartitions, std::vector< TreeNode const * > const &nodes)
	Find the smallest subtree (measured in number of nodes) that contains all given nodes. More...
std::vector< size_t >	get_clade_edges (Tree const &tree, std::vector< std::string > const &node_names)
std::vector< size_t >	get_clade_edges (Tree const &tree, std::vector< tree::TreeNode const * > const &nodes)
std::vector< size_t >	get_subtree_edges (TreeLink const &subtree)
utils::Bitvector	leaf_node_bitvector (Tree const &tree, std::vector< TreeNode const * > leaf_nodes)
	Return a Bitvector that has as many entries as the tree has leaf nodes, and is true where the given leaf_nodes are. More...
std::vector< size_t >	node_to_leaf_map (Tree const &tree)