biomcmc-lib  0.1
low level library for phylogenetic analysis
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1 /*
2  * This file is part of biomcmc-lib, a low-level library for phylogenomic analysis.
3  * Copyright (C) 2019-today Leonardo de Oliveira Martins [ leomrtns at; ]
4  *
5  * biomcmc is free software; you can redistribute it and/or modify it under the terms of the GNU General Public
6  * License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later
7  * version.
9  * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
10  * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
11  * details (file "COPYING" or
12  */
18 #ifndef _biomcmc_reconciliation_h_
19 #define _biomcmc_reconciliation_h_
21 #include "genetree.h" // genetree.c -> genetree.h, aux.h -> genetree.h
24 reconciliation new_reconciliation (int gene_nleaves, int sp_nleaves);
26 reconciliation new_reconciliation_from_reconciliation (int gene_nleaves, int sp_nleaves, reconciliation from);
31 void initialize_reconciliation_sp_count (reconciliation rec, int n_sp, int n_idx);
39 #endif
void del_reconciliation(reconciliation r)
release allocated memory for reconciliation_struct
Definition: reconciliation.c:69
mapping between gene tree nodes (this) and (external) species tree nodes
Definition: genetree.h:48
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...
Definition: reconciliation.c:47
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[]) ...
Definition: reconciliation.c:84
Definition: genetree.h:29
void reconciliation_gene_tree_reconcile(genetree gtre, speciestree sptre)
Find reconciliation map between gene and species trees.
Definition: reconciliation.c:157
gene tree and species tree structures, for reconciliation etc. This is the high-level file with globa...
void initialize_reconciliation_from_new_species_tree(genetree gtre, speciestree sptre)
transform indexes found in index_sptaxa_to_genetaxa() to pointers to species nodes ...
Definition: reconciliation.c:110
Definition: genetree.h:39
reconciliation new_reconciliation(int gene_nleaves, int sp_nleaves)
Allocate space for new reconciliation_struct (other functions defined in topology_mrca.c)
Definition: reconciliation.c:21