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<html>
<head>
<title>
SPACER - Principal Coordinate Analysis
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
SPACER <br> Principal Coordinate Analysis
</h1>
<hr>
<p>
<b>SPACER</b>
is a FORTRAN90 program which
reads a distance matrix and computes a principal coordinate analysis,
by Des Higgins.
</p>
<p>
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
<a href = "../../f_src/distances/distances.html">DISTANCES</a> program, which
converts a multiple alignment file into a distance matrix.
</p>
<h3 align = "center">
Languages:
</h3>
<p>
<b>SPACER</b> is available in
<a href = "../../f77_src/spacer/spacer.html">a FORTRAN77 version</a> and
<a href = "../../f_src/spacer/spacer.html">a FORTRAN90 version</a>.
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../f_src/distances/distances.html">
DISTANCES</a>,
a FORTRAN90 program which
can read a file in PIR format and create a distance matrix.
</p>
<p>
<a href = "../../f_src/read_align/read_align.html">
READ_ALIGN</a>,
a FORTRAN90 program which
can read a multiple sequence alignment file and write out the
relevant information into a file in PIR format.
</p>
<p>
<a href = "../../f_src/spacer_data_convert/spacer_data_convert.html">
SPACER_DATA_CONVERT</a>,
a FORTRAN90 program which
can read a multiple sequence alignment file and write out the
relevant information into a file in PIR format.
</p>
<h3 align = "center">
Author:
</h3>
<p>
Des Higgins, <br>
EMBL Data Library,<br>
April 1992
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
John Gower,<br>
Some distance properties of latent root and vector methods
used in multivariate analysis,<br>
Biometrika,<br>
Volume 53, 1966, pages 325-328.
</li>
<li>
Des Higgins,<br>
Sequence ordinations: a multivariate analysis approach
to analysing large sequence data sets,<br>
CABIOS,<br>
Volume 8, 1992, pages 15-22.
</li>
<li>
Brian Kernighan, Phillip Plauger,<br>
Software tools,<br>
Addison-Wesley, 1976,<br>
ISBN13: 978-0201036695,<br>
LC: QA76.6.K49.
</li>
<li>
<a href = "spacer.txt">spacer.txt</a>
the "readme" file for SPACER.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "spacer.f90">spacer.f90</a>, the source code;
</li>
<li>
<a href = "spacer.sh">spacer.sh</a>,
commands to compile and load the source code;
</li>
<li>
<a href = "spacer.txt">spacer.txt</a>, documentation;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<b>ALIGNMENT</b> uses data from a sequence alignment.
<ul>
<li>
<a href = "alignment_dist.txt">alignment_dist.txt</a>, the distance matrix
for an alignment;
</li>
<li>
<a href = "alignment_sym.txt">alignment_sym.txt</a>, symbols to use for plots;
</li>
<li>
<a href = "alignment_output.txt">alignment_output.txt</a>, the output from SPACER;
</li>
</ul>
</p>
<p>
<b>UKCITY</b> uses a distance matrix of driving times between
cities in the United Kingdom.
<ul>
<li>
<a href = "ukcity_dist.txt">ukcity_dist.txt</a>, the distance matrix;
</li>
<li>
<a href = "ukcity_sym.txt">ukcity_sym.txt</a>, symbols to use for plots;
</li>
<li>
<a href = "ukcity_output.txt">ukcity_output.txt</a>, the output from SPACER;
</li>
</ul>
</p>
<h3 align = "center">
List of Routines:
</h3>
<p>
<ul>
<li>
<b>SPACER</b> reads a euclidean distance matrix and outputs a PCOORD analysis.
</li>
<li>
<b>DIST_MAT_READ</b> reads the distance matrix from a file.
</li>
<li>
<b>EIGEN</b> computes the eigenvalues and eigenvectors of a symmetric matrix.
</li>
<li>
<b>EIGENSORT</b> sorts the eigenvalues and adjusts the eigenvectors.
</li>
<li>
<b>PCOORD</b> performs a principal coordinate analysis of distance matrix data.
</li>
<li>
<b>PLOTXY</b> creates a scatterplot of pairs of X, Y data.
</li>
<li>
<b>R_SWAP</b> switches two real values.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>TQLI</b> finds eigenvalues and eigenvectors of a real symmetric tridiagonal matrix.
</li>
<li>
<b>TRED2</b> tridiagonalizes a real symmetric matrix.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 20 October 2007.
</i>
<!-- John Burkardt -->
</body>
</html>