Proteins Case Study 

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This is an example of hierarchical cluster analysis using a published proximity matrix.  The proximities are distances for 20 species, in which the distance between two species is the number of positions in the protein cytochrome-c molecule where the proteins for the two species have different amino acids.

How we did it

The proximities were entered into a document using Word and copied to the Clipboard.  The matrix was then pasted into ClustanGraphics using File New Proximities.  The type of proximity measure as declared to be dissimilarity, and the matrix was then clustered using Average Linkage (UPGMA).  Labels and a title were entered in the Tree Labels dialogue and the file was saved as "Proteins.cls".

There is another example of clustering the data using Ward's Method, in Cluster Proximity Matrix.

The proximity matrix is reproduced from Hartigan J A, Clustering Algorithms, Wiley 1975, p. 209.  Hartigan states that the data were originally from Fitch and Margoliash, Science, 1967.

This dataset was featured in "POSTCARD FROM CLUSTAN", 1997.