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

Data Fields

int size
 
double ** d
 number of sequences to calculate distances
 
double mean_K2P_dist
 pairwise distance matrix (upper) and ti/tv rate ratio (lower triangle) for K2P formula for alignments
 
double var_K2P_dist
 average pairwise distance from K2P model
 
double mean_JC_dist
 variance in pairwise distance from K2P model
 
double mean_R
 average pairwise distance from JC model
 
double var_R
 average K2P transition/transversion ratio from pairwise distances
 
double freq [20]
 variance in K2P transition/transversion ratio from pairwise distances
 
double * fromroot
 empirical equilibrium frequencies
 
int * idx
 distance from root (used to calculate distance between tree leaves)
 
int * i_l
 
int * i_r
 
int ref_counter
 aux vectors for finding leaves spanned by subtrees on any node
 

The documentation for this struct was generated from the following file: