quick MP searches (was Bremer support)

[Leah Larkin]

Derek Sikes suggests an excellent strategy for avoiding swapping on
suboptimal islands in PAUP.  He gives directions for the search using
the graphical-user interface in the Mac version of PAUP.  The
following commands will do the exact same thing in the command-line
version.  I call this the "Bob Barker" approach (see Larkin et al.,
in press, Molecular Phylogenetic and Evolution), in honor of the
timeless "Price Is Right" strategy of bidding a dollar when you think
everyone else has overbid.

        hsearch enforce=no start=stepwise addseq=random nreps=10000
nchuck=5 chuckscore=1;
        hsearch enforce=no start=current chuckscore=no;

nchuck is the "X" in Derek's instructions
chuckscore is the "Y" (the $1 bid)

-Leah

>What a lot of people don't realize when using PAUP is that searches
>can spend (waste) large amounts of time on suboptimal islands/
>plateaus. This is why Rice et al.'s 1997 search using the rbcL 500
>dataset took 13 months. This problem can be avoided by using methods
>such as Nixon's Ratchet in NONA  (or use PAUPRat for PAUP), but even
>without the Ratchet PAUP can go much faster with the following search
>strategy:
>
>1. limit the number of trees swapped during each replicate to avoid
>swapping a suboptimal island to completion. This can be done in
>different ways. for example by setting in the branch swapping options
>(Mac version) the following: click the box to 'save no more than x
>trees > score y (each rep)' and set x to a number like 10 or 5 and y
>equal to either a known shortest score or simply 1. PAUP will then
>burn through all the reps very quickly but doing only quick searches
>in each rep. (for non-mac versions see the nchuck command in the
>reference guide).
>
>2. When done with step 1 use the best trees found as the starting
>trees for an unconstrained search that will explore all swapping
>options (swap each island to completion).
>
>The agony, if one watches the search progress closely, is seeing the
>search swapping for many days (or weeks) on, say a tree island with
>length 1287 and when it is done with that rep and begins the next it
>finds a tree island of length 1260 within minutes! This means all
>those days spent exploring that 1287 island were wasted. Use the
>above strategy to prevent this.
>
>Yours,
>-Derek
>
>On 30-Nov-05, at 1:11 PM, Karl Magnacca wrote:
>
>>I should clarify: it was NONA (which is also claimed to be much faster
>>than PAUP; it may be used as the regular search engine for TNT but
>>I'm not
>>sure) that ran so much slower.  The search that failed to find the
>>shortest trees in TNT was the special search technique for massive
>>data
>>sets.
>>
>>>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.
>>
>>What kind of computer are you using?  Unless it's a VIC-20, I can't
>>imagine it possibly taking that long for PAUP to run unless something
>>isn't working right.  The data set I was working with was 97 taxa,
>>~600
>>informative DNA and 15 morphological characters, and it only took 10
>>minutes for 100 replicates on a 266 Mhz computer.  On a new one it
>>takes
>>less than 2 minutes.
>>
>>Karl
>
>++++++++++++++++++++++++++++++++++++++++++++++
>Derek S. Sikes, Assistant Professor
>Division of Zoology
>Department of Biological Sciences
>University of Calgary
>2500 University Drive NW
>Calgary, Alberta, Canada, T2N 1N4
>
>dsikes at ucalgary.ca
>http://homepages.ucalgary.ca/~dsikes/sikes_lab.htm
>
>phone: 403-210-9819
>FAX:  403-289-9311
>
>"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
>
>Entomological Society of Alberta:
>http://www.biology.ualberta.ca/courses.hp/esa/esa.htm
>++++++++++++++++++++++++++++++++++++++++++++++


--
Leah Larkin, Ph.D.
Research Assistant Professor
Department of Biology
MSC03 2020, 167 Castetter Hall
1 University of New Mexico
Albuquerque, NM 87131-0001
(505) 277-2388 (Lab)    (505) 239-6036 (Cell)
(505) 277-4225 (Museum) (505) 277-0304 (FAX)