gene tree and species tree structures, for reconciliation etc. This is the high-level file with globally exposed functions/structures. More...

#include "upgma.h"

Include dependency graph for genetree.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	genetree_struct

struct	speciestree_struct

struct	reconciliation_struct
	mapping between gene tree nodes (this) and (external) species tree nodes More...

struct	splitset_struct

Typedefs
typedef struct genetree_struct *	genetree

typedef struct speciestree_struct *	speciestree

typedef struct reconciliation_struct *	reconciliation

typedef struct splitset_struct *	splitset

Functions
genetree	new_genetree_speciestree_pair (topology gene, topology species)

genetree	new_genetree (topology gene, speciestree sptre)
	Allocate space for new genetree_struct, given a gene topology and a specestree_struct.

void	del_genetree (genetree gtre)

speciestree	new_speciestree (topology species, int *order_of_species_names)
	Allocate space for new speciestree_struct, given a species topology and optionally the order of species names.

void	del_speciestree (speciestree sptre)

void	genetree_speciestree_distances (genetree gtre, speciestree sptre)
	calculates all (discrete) distances and update min and max

int	count_species_in_index_species_gene (int *sp_id, int max_sp, int n_sp_id)
	from gene-species map index, count number of distinct species represented

void	genetree_reconcile_speciestree (genetree gtre, speciestree sptre)
	<debug function>=""> dups.loss, ils calculation; accepts unseen speciestree_struct (i.e. updates mrca and pointers). Calls low-level hidden function.

void	genetree_dSPR_speciestree (genetree gtre, speciestree sptre, int level)
	<debug function>=""> dSPR (level > 1), hdist (level > 0), and RF distances; doesn't need to update sptree pointer

Detailed Description

gene tree and species tree structures, for reconciliation etc. This is the high-level file with globally exposed functions/structures.

Data Structures