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RE: Cladistics algorithm?



> From: owner-dinosaur@usc.edu [mailto:owner-dinosaur@usc.edu]On Behalf Of
> Rich Grenyer
>
> >However, the topic you are discussing is one of computer science and/or
> >computational phylogenetics, and not dinosaur science per se.  You should
> >seek out the various systematic discussion groups or
> computational science
> >groups for those details.
>
>
> Is this true? I know this list is volatile, and that
> cladistic/anti-cladistic/partially-cladistic/my-version-of-cladistic
> threads start up as soon as you look at them, but cladistics has had
> such an impact of dinosaurian phylogenetics and, hopefully, will
> continue to do so, that surely asking what the programs actually _do_
> is fair game? Is it likely anyone is going to initiate an in-depth
> discussion on ACCTRAN/DELTRAN optimisations, Dollo, Wagner or Fitch
> parsimony or Farris' Parsimony Jacknife? Goloboff's Ratchet
> implimentations? I hope not, because there are other lists better
> suited (and less interesting). But surely someone asking what
> fundamental cladistic algorithms actually _do_ is worthy of a reply
> and some pointers?

It was my impression that the question was essentially one of code: as in
"what precisely is the computer code that runs the analysis?"  If I was
wrong, please let me know.

However, in the short form:
You take a matrix of taxa and characters, filled with 0s, 1s, 2s, ?s etcs.;
You open that matrix in the software;
You choose one of various options (exact ones vary by program: in PAUP*
there is Heuristic, Branch-and-Bound, and Exhaustive Search; NONA has
Heuristic and Parsimony Rachet; etc.);
Using the particular batch of code, the software compares potential
alternative trees under some parameter (parsimony, maximum likelihood,
etc.), calculating (for example) tree length for each tree generated;
The software saves only the shortest trees (i.e., those with the lowest tree
length) (unless you ask it to save something else);
You then have a set of shortest trees, which then you can examine (i.e.: see
the topology of the trees; get certain tree statistics; etc.).

If the original poster wants more details on the exact nature of the various
options, I again  recommend going to a particular software package and
seeing the particular algorithm used.

Hope this helps.

                Thomas R. Holtz, Jr.
                Vertebrate Paleontologist
Department of Geology           Director, Earth, Life & Time Program
University of Maryland          College Park Scholars
                College Park, MD  20742
http://www.geol.umd.edu/~tholtz/tholtz.htm
http://www.geol.umd.edu/~jmerck/eltsite
Phone:  301-405-4084    Email:  tholtz@geol.umd.edu
Fax (Geol):  301-314-9661       Fax (CPS-ELT): 301-405-0796