SPACER
Principal Coordinate Analysis

SPACER is a FORTRAN77 program which 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.

Languages:

SPACER is available in a FORTRAN77 version and a FORTRAN90 version.

Related Data and Programs:

DISTANCES a program which can read a file in PIR format and create a distance matrix.

READ_ALIGN a program which can read a multiple sequence alignment file and write out the relevant information into a file in PIR format.

SPACER_DATA_CONVERT is a program which can read a multiple sequence alignment file and write out the relevant information into a file in PIR format.

Author:

Des Higgins,
EMBL Data Library,
April 1992

Reference:

1. John Gower,
   Some distance properties of latent root and vector methods used in multivariate analysis,
   Biometrika,
   Volume 53, 1966, pages 325-328.
2. Des Higgins,
   Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets,
   CABIOS,
   Volume 8, 1992, pages 15-22.
3. Brian Kernighan, Phillip Plauger,
   Software tools,
   Addison-Wesley, 1976,
   ISBN13: 978-0201036695,
   LC: QA76.6.K49.
4. spacer.txt the "readme" file for SPACER.

Source Code:

• spacer.f, the source code;
• spacer.sh, commands to compile and load the source code;
• spacer.txt, documentation;

Examples and Tests:

ALIGNMENT uses data from a sequence alignment.

• alignment_dist.txt, the distance matrix for an alignment;
• alignment_sym.txt, symbols to use for plots;
• alignment_output.txt, the output from SPACER;

UKCITY uses a distance matrix of driving times between cities in the United Kingdom.

• ukcity_dist.txt, the distance matrix;
• ukcity_sym.txt, symbols to use for plots;
• ukcity_output.txt, the output from SPACER;

List of Routines:

• 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.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• TQLI finds eigenvalues and eigenvectors of a real symmetric tridiagonal matrix.
• TRED2 tridiagonalizes a real symmetric matrix.

You can go up one level to the FORTRAN77 source codes.