1 #ifndef GENESIS_TREE_BIPARTITION_FUNCTIONS_H_ 2 #define GENESIS_TREE_BIPARTITION_FUNCTIONS_H_ 59 utils::Bitvector
leaf_node_bitvector( Tree
const& tree, std::vector<TreeNode const*> leaf_nodes );
75 std::vector<Bipartition>
const& bipartitions,
76 std::vector<TreeNode const*>
const& nodes
112 std::vector<Bipartition>
const& bipartitions,
113 std::vector<TreeNode const*>
const& nodes,
114 bool include_splitting_edges =
true,
115 bool include_leaf_edges =
true 120 std::vector<TreeNode const*>
const& nodes,
121 bool include_splitting_edges =
true,
122 bool include_leaf_edges =
true 128 bool include_splitting_edges =
true,
129 bool include_leaf_edges =
true 138 std::vector< tree::TreeNode const* >
const& nodes
149 #endif // include guard 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.
std::vector< size_t > get_clade_edges(Tree const &tree, std::vector< tree::TreeNode const * > const &nodes)
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 l...
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
std::vector< size_t > node_to_leaf_map(Tree const &tree)
std::vector< Bipartition > bipartition_set(Tree const &tree)
std::vector< size_t > get_subtree_edges(TreeLink const &subtree)
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, bool include_leaf_edges)
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.
std::vector< std::string > node_names(Tree const &tree, bool leaves_only)
Returns a list of all TreeNode names of a Tree.