Definitions for

**"Distance matrix"**A table showing the evolutionary distances between all pairs of nucleotide sequences in a dataset.

Matrix which visualizes the calculation of the score of an optimal pairwise alignment (i.e. distance) of sequences or other attributes. Distances are small for similar sequences. The Protdist program we use computes a distance measure for protein sequences, using maximum likelihood estimates based on a particular matrix that indicates the significance of certain amino acid changes.

a matrix that lists the shortest paths between each node of the hypertext (if one exists)