biomcmc-lib  0.1
low level library for phylogenetic analysis
Data Structures | Typedefs | Functions
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_structbinary_parsimony_datamatrix
 
typedef struct binary_parsimony_structbinary_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