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Re: Cladistics algorithm?

So, for example, a paleontologist might need to specify not only his CONCLUSION,
but also
1) the name of the software used
2) the setting of the software
3) the version of the software (do they ever update them and the underlying
algorithms? and are there proper names for these algorithms like, say "Fred's
Formula" or "Manny's Method?")

OK: with you up to here. Yes, phylogenetic packages are _always_ being updated to implement new methods and improves old ones. In the main, these updates are transparent and explicit; right down to the code level sometimes.

4) in what direction the data is "weighted" during input
5) how much post-analytical "blurring" is done.

All the opinions are all very well and good, I'd just like to understand what is
behind them in the same way that I'm able to get the sample size and the double
or triple blinding data on a good medical study.


And there's no reason why you can't with phylogenetics. Any decent publication that performs a phylogenetic analysis should detail the packages, versions and procedures (and yes, this included software options used), together with access to the data matrix used and details of character coding methods. The necessity for others to replicate your results isn't just something that applies to other branches of science.

It APPEARS to me that that the variables and constants here are having a lot of
smoke blown around them and the original question was to try to understand the
precise algorithms to begin with and to see if the variant algorithms are really
identical, equivalent, or have inherent differences that ought to be considered
in conversation.

This is in danger of becoming combustible, but the exact algorithms that are implemented in major phylogenetics packages are extremely well understood, and have been for many years now - your variables and constants, if I undertand you correctly, are all there in plain view. Alas, the alogrithms are commonly mathematically obtuse, and procedurally complex. They are also often layered with jargon; this isn't a bad thing, but can make them difficult to pick up quickly from fresh. Start with simple parsimony (try those references I posted earlier); it's pretty simple philosophically and is fundamentally practical in nature. Try one on your own specimens; if not, make some up, go through some late 80's phylogenetics papers, code your family, get hold of the Caminicules and try coding them - anything. It's not at all opaque when you use it for a while.


Rich Grenyer

Mammalian Evolution and Conservation
Biology Department
Imperial College at Silwood Park

Telephone: +00 44 (0)20 7594 2328
Fax:            +00 44 (0)20 7594 2339
email: r.grenyer@ic.ac.uk