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

[Sergio Vargas]

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