[Taxacom] cladistics (was: clique analysis in textbooks)

[John Grehan]

 It was interesting to see that Sergio's perspective was no the only one made on the list concerning clustering. It is evident that my sue of clustering was more objectionable to some than to others, as seems to be the usual case over terminology in general.

When one arranges A with B rather than either with C, that is clustering as far as I am concerned - however it is generated.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Sergio Vargas
Sent: Friday, August 19, 2011 2:32 PM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] cladistics (was: clique analysis in textbooks)

Hi,

 >Clustering is clustering is clustering. Group some things together and you are clustering - however it is done.

no you are not. Grouping is not clustering, there are many ways to group things together not involving clustering. Maximum parsimony, maximum likelihood and bayesian analysis are not clustering. It is simply incorrect to call to these methods clustering. When you run either of the above analyses you are not clustering, despite the result being something similar to a cluster. If you could reduce phylogenetic inference to clustering everything would be so easy (computationally
speaking) because clustering can be done (computationally) efficiently whereas searching for an optimal tree using phylogenetic methods cannot. 
Taxa are only "clustered" (randomly or sequentially) together to build the first tree, afterwards entire topologies are evaluated, taxa are not clustered. This is so basic I cannot believe I am explaining it.

sergio

--
Sergio Vargas R., M.Sc.
Dept. of Earth&  Environmental Sciences
Palaeontology&  Geobiology
Ludwig-Maximilians-Universität München
Richard-Wagner-Str. 10
80333 München
Germany
tel. +49 89 2180 17929
s.vargas at lrz.uni-muenchen.de
sevra at marinemolecularevolution.org

check my webpage:
http://www.marinemolecularevolution.org

check my research ID:
http://www.researcherid.com/rid/A-5678-2011


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