Bremer support

[James Zahniser]

Well, I suppose different data sets will run differently, but in my original search for MP trees, an approximately 30-minute search in TNT yielded the same set of MP trees as the search in PAUP (500 random addition sequences, TBR branch swapping) which took *almost 2 weeks* for a data set with 68 taxa and 120 morphological characters.  This is not to say that I won't use PAUP in the future (it's obviously a wonderful program and can do a lot of things that TNT can't), but I think TNT is worth exploring.

    James N. Zahniser
Department of Entomology
University of Illinois at Urbana-Champaign
320 Morrill Hall
505 S. Goodwin Ave.
Urbana, IL  61801


  On 28 Nov 2005 at 20:56, James Zahniser wrote:
> I have used Goloboff et al's program TNT.  It runs very quickly and
> is fairly user friendly.  You constrain nodes by interfacing with
> your tree of choice and run an analysis for each constraint.  It is a
> little repetitive to run analyses for each constrained node, but far
> quicker than with traditional searches.

I should point out, however, that most of the boasts about TNT are
overblown.  I ran it against Paup on three different computers and
found
that TNT took between two and ten times as long (depending on the
processor speed of the computer).  It's supposed to be best on large
data sets but doesn't always find the shortest trees in that case.

> Those more computer-savvy than me might know how to run a batch file
to
> compute support for all nodes with a set of runs.

There is a program called AutoDecay that will generate constraint trees
for all nodes.  It runs off Paup but it's easy to convert a file of
Paup
trees to Hennig86/Nona format (which I believe is used by TNT as well)
using search and replace.

Karl
=====================
Karl Magnacca, USGS-BRD
PO Box 11, Hawaii Natl. Park, HI 96718
"Democracy used to be a good thing, but now it has
gotten into the wrong hands."   --Sen. Jesse Helms



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