parsimony.h File Reference

binary and multistate parsimony matrices, together with bipartition extraction for MRP More...

#include "topology_distance.h"

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Data Structures
struct	binary_parsimony_datamatrix_struct
	used by matrix representation with parsimony (01 10 11 sequences) More...
struct	binary_parsimony_struct

Typedefs
typedef struct binary_parsimony_datamatrix_struct *	binary_parsimony_datamatrix
typedef struct binary_parsimony_struct *	binary_parsimony

Functions
binary_parsimony_datamatrix	new_binary_parsimony_datamatrix (int n_sequences)
binary_parsimony_datamatrix	new_binary_parsimony_datamatrix_fixed_length (int n_sequences, int n_sites)
void	del_binary_parsimony_datamatrix (binary_parsimony_datamatrix mrp)
binary_parsimony	new_binary_parsimony (int n_sequences)
binary_parsimony	new_binary_parsimony_fixed_length (int n_sequences, int n_sites)
void	del_binary_parsimony (binary_parsimony pars)
void	update_binary_parsimony_from_topology (binary_parsimony pars, topology t, int *map, int n_species)
	given a map[] with location in sptree of gene tree leaves, update binary matrix with splits from genetree
int	binary_parsimony_score_of_topology (binary_parsimony pars, topology t)
void	pairwise_distances_from_binary_parsimony_datamatrix (binary_parsimony_datamatrix mrp, double **dist, int n_dist)

Detailed Description

binary and multistate parsimony matrices, together with bipartition extraction for MRP