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:

Data Fields