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This section focuses first on how we estimate distances, depending upon the level of interest, and then highlights some approaches for visualizing and gaining inferences from the distance matrix itself.
A distance-heredity graph, also known as a completely separable graph, is a graph G such that the distance matrix of every connected vertex-induced subgraph G_V of G is the submatrix obtained from the distance matrix of G itself corresponding to the subset of vertices V.
The distance matrix is widely used in the bioinformatics field, and it is present in several methods, algorithms and programs. Distance matrices are used to represent protein structures in a coordinate-independent manner, as well as the pairwise distances between two sequences in sequence space.
The Distance Matrix. Suppose that we have a group of three observations where each observation is a vector with three components. We can write this set of observations as a 3 x 3 matrix A where each row represents one observation.
The Geographic Distance Matrix Generator is a platform-independent Java application that implements the same powerful suite of spherical functions as the Perpendicular Distance Calculator to compute all pair wise distances from a simple list of geographic coordinates.
The book is organized into 10 chapters covering mathematical topics in relation to genetic code systems, biological sequences, structures and functions, networks and biologi-cal systems, matrix genetics, cognitive informatics, and the central dogma of informatics.
Genetic distance calculation. Fast pairwise distance estimation; Computing genetic distances using the Alignment object; Using the distance calculator directly; Likelihood based pairwise distance estimation; Get the names of sequences with max pairwise distance; Get the names of sequences with min pairwise distance
