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"Classification, clustering, and phylogeny estimation" <[log in to unmask]>
Fionn Murtagh <[log in to unmask]>
Sat, 30 Sep 2006 15:59:12 +0000
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"Classification, clustering, and phylogeny estimation" <[log in to unmask]>
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Hi Bill,

A simple algorithm is the bond energy algorithm - references include

c     Bond energy algorithm -- see:
c     (1) W.T. McCormick, P.J. Schweitzer and T.W. White,
c         "Problem decomposition and data reorganization by a clustering
c         technique", Oper. Res., vol. 20, pp. 993-1009, Sept./Oct. 1972.
c     (2) P. Arabie and L.J. Hubert,
c         "The bond energy algorithm revisited", IEEE Trans. Syst. Man
c         Cybern., vol. 20, pp. 268-274, 1990.
c     (3) P. Arabie, S. Schleutermann, J. Daws and L. Hubert,
c         "Marketing applications of sequencing and partitioning of
c         nonsymmetric and/or two-mode matrices", in W. Gaul and M. Schader,
c         Eds., Data Analysis, Decision Support, and Expert Knowledge
c         Representation in Marketing, Springer Verlag, 1988, pp. 215-224.

and I have a program for it in Fortran (sorry...!  It's quite simple and 
would not be difficult for someone to recode) at
(My multivariate software entry page is

I hope this helps.  The association with using a wavelet transform was
F. Murtagh, J.-L. Starck and M. Berry, "Overcoming the curse of 
dimensionality in clustering by means of the wavelet transform", The 
Computer Journal, 43, 107-120, 2000.

fmurtagh at acm . org
(This hotmail account is not for general use - most messages deleted 

From: shannon <[log in to unmask]>
Reply-To: "Classification, clustering, and phylogeny estimation"             
  <[log in to unmask]>
To: [log in to unmask]
Subject: sorting datafiles
Date: Thu, 28 Sep 2006 16:36:48 -0500

We are looking for an algorithm that sorts a datafile by columns and rows
simulataneously.  We implemented this a few years ago but I can't remember
where the code might have gone (I'm guessing it left with my memory).

I believe Fionn used something like this to rearrange datafiles to be
'image-like' for wavelet trasnform (Fionn, ring a bell).

Would appreciate any help on finding the algorithm.


		        Biostatistics Consulting Center

"Statistics is not a discipline like physics, chemistry or biology
where we study a subject to solve problems in the same subject. We
study statistics with the main aim of solving problems in other
disciplines."   CR Rao

William D. Shannon, Ph.D.

Associate Professor of Biostatistics in Medicine
Division of General Medical Sciences and Biostatistics

Washington University School of Medicine
Campus Box 8005, 660 S. Euclid
St. Louis, MO   63110

Phone: 314-454-8356
Fax: 314-454-5113
e-mail: [log in to unmask]
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