Clusterer
A pair clustering algorithm in PHP. Released under the MIT license.

To install: pear install channel://ardell.pearfarm.org/Clusterer

This algorithm takes pair data, for instance "a is near b" and "b is near c" to produce clusters (a, b, c).

Input should be provided as an array of 2 item arrays, e.g:
$pairs = array(
    array('a', 'b'),
    array('b', 'c'),
    array('d', 'e'),
    array('d', 'f'),
    array('g', 'h')
)

Clusterer::cluster($pairs); // will return...
array(
    array('a', 'b', 'c'),
    array('d', 'e', 'f'),
    array('g', 'h')
)

Thanks to Alan Pinstein for help developing and writing the algorithm.