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Heuristic searches

newsmgr at merrimack.edu newsmgr at merrimack.edu
Mon Apr 13 18:56:57 EST 1998

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Newsgroups: bionet.molbio.evolution
Subject: Re: Heuristic searches
Message-ID: <harshman.diespamdie-1204981306220001 at pm5-61.sfo.infi.net>
From: harshman.diespamdie at sjm.infi.net (John Harshman)
Date: 12 Apr 1998 21:05:12 GMT
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In article <6gdsie$jmv at net.bio.net>, "Dr. Andrew G. McArthur"
<mcarthur at onyx.si.edu> wrote:

> Colleagues & Dr. Sikes,
> This is indeed a valid and useful method, one that I have been using for
> some time.  The bonus in speed is wonderful.  By limiting replicates to
> keeping only a small number of trees in memory (I use 20), the random
> replicates search gathers a good sampling of the various parsimonious
> islands.  These islands have not been searched extensively - tree #21 may
> have swapped to a more parsimonious topology.  But, by keeping the trees in
> memory and doing exhaustive TBR swapping on them in a second heurstic
> search, you ensure that PAUP will find all parsimonious trees instead of
> just getting stuck in a single island.  This approach gives you a good
> coverage of the parsimony surface while still being robust.

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.

You should find it easy to locate many papers that use or advocate this
method. Try searching Systematic Biology for the last several years. I
particularly remember the paper in which the data for human mtDNA
sequences were reanalyzed.

> At 10:16 AM 4/7/98 -0500, you wrote:
> >To those experienced with heuristic searching using PAUP*:
> >
> >I have stumbled upon what seems to be a means by which shortest trees can 
> >be found far quicker and with high confidence than by the method I 
> >previously used.
> >So I examined the PAUP heuristic searching options and one option allows 
> >users to limit the number of trees found for a single replicate before 
> >starting another replicate.  Therefore, if one's dataset allows many mpts 
> >(which take hours to days to swap) one can set a limit of say 100 trees 
> >or 50 trees saved per "island".  With this setting PAUP can crank through 
> >100 or even 200 replicates in a few hours-(and, of course, if one wants 
> >to wait a few days one can get a few thousand replicates completed)
> >
> >PAUP  will save the shortest trees in memory and once the run is complete 
> >you can start the search again specifying that PAUP use the "trees in 
> >memory" as the starting trees.  This will result in complete swapping on 
> >the "best" island(s) yielding all the mpts of that length (and maybe  
> >some shorter...).


Just a couple more things:
   *Note the obvious spam-defeating modification
    to my address if you reply by email.
   *It's my belief that my posts are now making it into talk.origins
    But anyway: if you read this in somebody else's post but never
    saw my original, please tell me. If you got this in email and
    respond in TO, please retain this part of my sig.

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