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In mathematics, a Euclidean distance matrix is an n×n matrix representing the spacing of a set of n points in Euclidean space. For points x 1 , x 2 , … , x n {\displaystyle x_{1},x_{2},\ldots ,x_{n}} in k -dimensional space ℝ k , the elements of their Euclidean distance matrix A are given by squares of distances between them.
In general, a distance matrix is a weighted adjacency matrix of some graph. In a network, a directed graph with weights assigned to the arcs, the distance between two nodes of the network can be defined as the minimum of the sums of the weights on the shortest paths joining the two nodes (where the number of steps in the path is bounded). [2]
The distance between two objects that are not points is usually defined to be the smallest distance among pairs of points from the two objects. Formulas are known for computing distances between different types of objects, such as the distance from a point to a line.
Except for the final row and column of 1s, the matrix in the second form of this equation is a Euclidean distance matrix. Compare this to the usual formula for the oriented volume of a simplex , namely 1 n ! {\displaystyle {\tfrac {1}{n!}}} times the determinant of the n x n matrix composed of the n edge vectors A 1 − A 0 , … , A n − A 0 ...
The distance (or perpendicular distance) from a point to a line is the shortest distance from a fixed point to any point on a fixed infinite line in Euclidean geometry. It is the length of the line segment which joins the point to the line and is perpendicular to the line. The formula for calculating it can be derived and expressed in several ways.
The distance matrix can come from a number of different sources, including measured distance (for example from immunological studies) or morphometric analysis, various pairwise distance formulae (such as euclidean distance) applied to discrete morphological characters, or genetic distance from sequence, restriction fragment, or allozyme data.
For a fixed length n, the Hamming distance is a metric on the set of the words of length n (also known as a Hamming space), as it fulfills the conditions of non-negativity, symmetry, the Hamming distance of two words is 0 if and only if the two words are identical, and it satisfies the triangle inequality as well: [2] Indeed, if we fix three words a, b and c, then whenever there is a ...
The Robinson–Foulds or symmetric difference metric, often abbreviated as the RF distance, is a simple way to calculate the distance between phylogenetic trees. [1]It is defined as (A + B) where A is the number of partitions of data implied by the first tree but not the second tree and B is the number of partitions of data implied by the second tree but not the first tree (although some ...