SPACER - Principal Coordinate Analysis

SPACER is a program that reads a distance matrix and computes a principal coordinate analysis. Along with numerical data, a crude TTY plot of the first principal axis versus the second and third is printed. The distance matrix data may be prepared by the DISTANCES program, which converts a multiple alignment file into a distance matrix.

Author:

Des Higgins,
EMBL Data Library,
April 1992

Files you may copy include:

• spacer.f90, the source code;
• spacer.txt, documentation;
• alignment.dis, the distance matrix for an alignment;
• alignment.sym, symbols to use for plots;
• alignment.out, the output from SPACER;
• ukcity.dist, the distance matrix for UK city travel times;
• ukcity.sym, symbols to use for plots;
• ukcity.out, the output from SPACER;

The list of routines includes:

• SPACER reads a euclidean distance matrix and outputs a PCOORD analysis.
• DIST_MAT_READ reads the distance matrix from a file.
• EIGEN computes the eigenvalues and eigenvectors of a symmetric matrix.
• EIGENSORT sorts the eigenvalues and adjusts the eigenvectors.
• PCOORD performs a principal coordinate analysis of distance matrix data.
• PLOTXY creates a scatterplot of pairs of X, Y data.
• R_SWAP switches two real values.
• TQLI finds eigenvalues and eigenvectors of a real symmetric tridiagonal matrix.
• TRED2 tridiagonalizes a real symmetric matrix.

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