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

#include <genetree.h>

Collaboration diagram for reconciliation_struct:

Data Fields
topol_node *	map_d

topol_node *	map_u
	Mapping of all nodes from gene to species (the first gene::nnodes are fixed)

int *	sp_id
	Mapping of all nodes from gene to species, assuming gene tree is upside down (unrooted TESTING version)

int *	sp_count
	mapping of gene (this tolopogy) leaf to ID of taxon in species tree

int	sp_size
	how many copies of each species are present in this gene (used by deepcoal)

int	size_diff
	effective number of species present in gene family

int *	dup
	twice the difference in number of leaves between gene tree and (reduced/effective) species tree

int *	ndup_d
	indexes of duplication nodes on gene tree, and number of such nodes (unused for now)

int *	ndup_u
	number of duplications below node (edge above node, since struct assume node == edge above it)

int *	nlos_d
	number of duplications above node (edge upside down, thus "children" are 'up' and 'sister')

int *	nlos_u
	number of losses below node and edge above node

int	ndups
	number of losses above node, including edge above it

int	nloss
	minimum number of duplications over all possible rootings, acc. to reconciliation_struct::dup

int	ndcos
	number of losses corresponding to rooting (edge) that minimizes duplications

Detailed Description

mapping between gene tree nodes (this) and (external) species tree nodes

The documentation for this struct was generated from the following file:

Data Fields