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RE: Cladistics algorithm?

Can anyone supply the algorithm (or algorithms) that are used for
cladistic analysis?

By way of further clarification or to confuse it even more (depending on
how you view this), there are, apparently, a number of "black box"
softwares that contain such an algorithm and into which aspiring
cladists can pump very statistics to receive an analysis.  What goes on
in that black box?


Almost every phylogenetics package is listed here by Joe Felsenstein at Washington.


The black-box remark is commonplace, and generally wrong. Almost every package wil contain documentation that expicitly states what the program will do (although admittedly, the details of methods a given program implements may well require reference to an original paper). Of course, if people use it as a black-box, then that's up to them. The output will generally reflect the knowledge of the user.

A basic knowledge of elementary cladistics (including really fundamental algorithms) can be obtained from any number of sources; my own favourites are the Compleat Cladist (available free and online at http://nhm.ukans.edu/cc.html). Books: Cladistics by Kitching et al (http://www.oup.co.uk/isbn/0-19-850138-2) or Molecular Systematics by Hillis et al. (http://www.sinauer.com/Titles/Text/hillis.html).