reweighting characters, few and many
termites at USP.BR
Wed Oct 27 10:54:07 CDT 1999
Already a few months ago, an anonymous list member told me that cladistics
functions like that: Figure out a tree that you personally like! In the next
step choose a suitable program and algorithm which generate exactly this tree.
Yesterday, at night, I made my first exciting experiences of this kind.
In PAUP 4.0, I ran a matrix which gave 423 most parsimonious trees. As the
consensus tree was highly unresolved, I ran the command "reweight" which gave,
after a new search, 21 parsimonious trees, and a nice consensus tree, but one
that I personally dislike.
So, in the next step I widened up slightly, but only slightly, the upper bound
of the trees to be kept and searched the unweighted characters again.
Excitingly, this enlargened the tree file from 423 trees to approximately 25000
trees. Now, I reweighted those 25000 trees, and run parsimony search again.
I got only three trees, and Imagine!!!, the consensus tree corresponds exactly
to the tree, which is my person favourite!!!
Any suggestions? Thomas
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