biomcmc-lib  0.1
low level library for phylogenetic analysis
Data Fields
reconciliation_struct Struct Reference

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

#include <genetree.h>

Collaboration diagram for reconciliation_struct:
Collaboration graph

Data Fields

 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: