Max Like for Amino Acid seqs

Byron Adams bjadams at CRCVMS.UNL.EDU
Mon Sep 23 14:23:54 EST 1996


>In Article <Pine.A32.3.91.960919094515.27528A-100000 at gsaix2.cc.GaSoU.EDU>,
>qfang at GSAIX2.CC.GASOU.EDU ("Q. Quentin Fang") wrote:
>>How about Puzzle 2.5, a maximum likelihood program for both nucleotides and
>>a.a.?  Has anyboy tried the program?
>>
>>+=====================================+
>>  Q. Quentin Fang, Ph.D.
>>
>Hello  Quentin.
>
>I use the program and really like it, easy to use, works nicely w/ CLUSTALW,
>etc.  The only caveate is that it runs a little slow, takes about 8 hours
>for 70 100 AA length species, using a unix box.  I dont think most people
>use that many species.  If you have, say, one of the really beefy RISC-based
>Power Macs (eg 200 mhz 603e or 604e) this probably only takes about an hour.
>Ah, to have alot of money.
>
>Ralph

Ralph & Quentin:

        On a 132 mhz Power PC, Puzzle 2.5 took 1.5 hours for 15 taxa and
641 amino acid sites; fast for a reasonably sized data set.

Byron

______________________________________________________________________________
Byron J. Adams
University of Nebraska
406 Plant Sciences Hall
P.O. Box 830722
Lincoln, NE 68583-0722
(402) 472-2858                      "Wilderness, once we have given
fax (402) 472-2853                   it up, is beyond our
bjadams at crcvms.unl.edu               reconstruction."
                                         -Wallace Stegner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"Evolution is a change from a nohowish, untalkaboutable all-alikeness, to a
somehowish and ingeneral-talkaboutable, not-all-alikeness, by continuous
somethingelsifications and stick-togetherations."
        -a mathmatician named Kirkman

(from Tait, P. G.  1880. "Prof. Tait on the Formula of Evolution."  Nature,
(23)pp.80-82.  [from Dennet, D. C.  1995, p393.  Darwin's Dangerous Idea:
Evolution and Meanings of Life.  Simon & Schuster, New York, NY.
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