topology_randomise.h File Reference

Creation of random topologies and modification of existing ones through branch swapping. More...

#include "topology_distance.h"
#include "prob_distribution.h"

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Functions
void	randomise_topology (topology tree)
	low level function that generates a random tree (equiv. to random refinement of a star topology)
void	quasi_randomise_topology (topology tree, int sample_type)
	generates a random topology if sample_type==0, but can reuse some info later to create a "correlated" tree
void	create_parent_node_from_children (topology tree, int parent, int lchild, int rchild)
	create internal node with given children (children coalesce into parent node)
void	topology_apply_rerooting (topology tree, bool update_done)
	random rerooting
void	topology_apply_shortspr (topology tree, bool update_done)
	recursive SPR over all internal nodes, assuming common prob of swap per node
void	topology_apply_shortspr_weighted (topology tree, double *prob, bool update_done)
	recursive SPR over all internal nodes, using prob[] vector as rough guide of error rate for node
void	topology_apply_spr_on_subtree (topology tree, topol_node lca, bool update_done)
	random Subtree Prune-and-Regraft branch swapping for subtree below lca node
void	topology_apply_spr (topology tree, bool update_done)
	random Subtree Prune-and-Regraft branch swapping
void	topology_apply_spr_unrooted (topology tree, bool update_done)
	random Subtree Prune-and-Regraft branch swapping generalized (neglecting root)
void	topology_apply_nni (topology tree, bool update_done)
	random Nearest Neighbor Interchange branch swapping (SPR where regraft node is close to prune node)
bool	cant_apply_swap (topology tree)
	check if it is possible to apply SPR/NNI without rerooting (used by topology_apply_spr() and MCMC functions)

Detailed Description

Creation of random topologies and modification of existing ones through branch swapping.