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:

Examples and Tests:

ALIGNMENT uses data from a sequence alignment.

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

List of Routines:

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


Last revised on 25 June 2008.