well-supported parts of cladograms

James B. Whitfield jwhitfie at COMP.UARK.EDU
Thu Sep 11 11:39:22 CDT 1997


Dear Richard and other Taxacomers on the "probabilities" thread...

        Richeard Zander wrote:

"  Also, if my shortest tree isn't well-supported, I'd like to identify
portions of the cladogram that have more evidence for than against. (I
think this is what people mean by "we don't think our cladograms are
necessarily exactly right, but they are probably mostly right." Surely
one can provide a measure of how right various subclades are other than
the open ended ones of Bremer support, etc.)"

        You might wish to explore the use of spectral analysis (using the
Hadamard conjugation).  The computer program Spectrum (and others, they are
continually being improved to handle 4-state characters, etc.) is available
from Mike Charleston's site at
http://taxonomy.zoology.gla.ac.uk/mike/mike.html

        This method splits the analysis/evidence into evidence for/against
each possible way of splitting into clades, so you can (if you use graphs)
visually assess which clades have the most overall support.  There are also
ways of using this information to feed back into tree estimation, but I
find it most useful at present for data exploration (i.e., examining which
clades have the most support AND whether the data are too noisy to be able
to settle on ANy coherent pattern).

                                                        Cheers, Jim Whitfield

J. B. Whitfield
Department of Entomology
University of Arkansas
Fayetteville, AR 72701
(501)575-2482 FAX -2452
jwhitfie at comp.uark.edu




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