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Re: Cladistics algorithm?
So, for example, a paleontologist might need to specify not only his
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
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
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.
Mammalian Evolution and Conservation
Imperial College at Silwood Park
Telephone: +00 44 (0)20 7594 2328
Fax: +00 44 (0)20 7594 2339