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heuristic searches

Sikes dss95002 at uconnvm.uconn.edu
Tue Apr 14 10:36:42 EST 1998


Colleagues,

>This method is advocated and used by lots of people, including the
>Maddision brothers. I use it too, and I set the number even lower, usually
>from 2 to 5. If you want to spend more time, it's better to add random
>addition replicates than to increase the number of trees per replicate.


This procedure may greatly speed the finding of the shortest tree length 
for one's dataset but my concern is that once that tree length is found, 
how confident can one be about finding ALL the trees of that length?

I would guess that some fraction of the equally parsimonious trees would 
be missed by not searching each island to completion and thus one's 
consensus tree would be an inaccurate representation of the quality of 
one's dataset.  Can someone refute this with data (rather than opinion)?

It would appear that some careful, controlled experiments should be 
performed to see what the drawbacks are (if there are any)...[as an aside 
it is interesting to note the lack of studies addressing the problem of 
large dataset tree searching in comparison to the number of studies 
dealing with branch support questions for smaller datasets.  Of course, a 
strict consensus of many mpts is a type of  branch support measure..]

Yours,

Derek S. Sikes




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Derek Sikes
Dept. of Ecology and Evol. Biology U-43
University of Connecticut
Storrs, CT 06269  USA

dss95002 at uconnvm.uconn.edu
http://www.eeb.uconn.edu/grads/sikes.htm

"Remember that Truth alone is the matter you are in Search after; and if 
you have been mistaken, let no Vanity reduce you to persist in your 
mistake." Henry Baker, London, 1785
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