18 #ifndef _biomcmc_topology_distance_h_ 19 #define _biomcmc_topology_distance_h_ 37 void estimate_topology_branch_lengths_from_distances (
topology tree,
double *dist);
38 double* new_topology_branch_lengths_from_distances (
topology tree,
double *dist);
39 void correct_negative_branch_lengths_from_topology (
topology t,
double *blength);
void patristic_distances_from_topology_to_vectors(topology tree, double **dist, double *scaling, int n_dists, double tolerance)
calculates rescaled patristic distances returning up to 6 distinct 1D vectors #dist (externally alloc...
Definition: topology_distance.c:81
General-purpose topology structures created from nexus_tree_struct (and low-level functions) ...
void fill_distance_matrix_from_topology(distance_matrix dist, topology tree, double *blen, bool use_upper)
fill in distance_matrix with the patristic distances from topology (can be used with distinct branch ...
Definition: topology_distance.c:37
distance_matrix new_distance_matrix_for_topology(int nleaves)
allocate memory for a new distance_matrix that will be used on topologies
Definition: topology_distance.c:23
int * create_vector_with_idx_leaves_below_for_patristic(topology tree)
similar to an Euler tour, has list of leaves below each node
Definition: topology_distance.c:118
Definition: distance_matrix.h:29
Binary unrooted topology (rooted at leaf with ID zero)
Definition: topology_common.h:47