reconciliation.h File Reference

low-level file for gene tree and species tree reconciliation. This file is hidden from user and contains the LCA-based reconciliation distances. More...

#include "genetree.h"

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Functions
reconciliation	new_reconciliation (int gene_nleaves, int sp_nleaves)
	Allocate space for new reconciliation_struct (other functions defined in topology_mrca.c)
reconciliation	new_reconciliation_from_reconciliation (int gene_nleaves, int sp_nleaves, reconciliation from)
	Create new reconciliation struct and copy values (except species tree info) from another struct.
void	del_reconciliation (reconciliation r)
	release allocated memory for reconciliation_struct
void	initialize_reconciliation_sp_count (reconciliation rec, int n_sp, int n_idx)
	Fill rec->sp_count[] with the number of representatives of each species (idexed by rec->sp_id[])
void	initialize_reconciliation_from_new_species_tree (genetree gtre, speciestree sptre)
	transform indexes found in index_sptaxa_to_genetaxa() to pointers to species nodes
void	reconciliation_gene_tree_reconcile (genetree gtre, speciestree sptre)
	Find reconciliation map between gene and species trees.

Detailed Description

low-level file for gene tree and species tree reconciliation. This file is hidden from user and contains the LCA-based reconciliation distances.