By about now a summer-1994 version of PAUP (by David Swofford) was
supposed to be coming out from some unspecified vendor.
Has anybody out there heard about this actually happening?
My current version of PAUP (v3.0o) is four years old and, while useful,
has got some serious bugs. First of all, its imposition of topological
constraints upon exhaustive tree-searches appears to be horribly inaccurate
-- it cannot seem to actually *comprehend* polytomies, which is after all
what one generally wants to be part of any topological constraint in the
first place. Furthermore, it is completely incapable of generating random
trees. Since I am trying to statistically analyse the phylogenetic signal
present in 12 sequence motifs from divergent proteins (by calculating the
treelength-skew that remains inherent in the primary data, after various
minimal topological conditions have been imposed on the trees they can
yield), these handicaps are crippling.
If anybody knows of how I can get a better version than v3.0o, I would
thus be quite grateful for their advice, either via posting here or via
e-mail. (For that matter, I would be at least partially satisfied merely
to obtain a *user's* manual that was written after 1990...)
Thank you very much in advance.
Division of Biology
California Institute of Technology
e-mail: schwarze.ccomail at starbase1.caltech.edu