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PAUP on Power Macintosh

MANHART, JAMES j0m1742 at venus.tamu.edu
Tue Mar 15 14:33:00 EST 1994

I just ran a comparative test on several types of Macs using
PAUP 3.1.1 with a data set that contained 34 rbcL sequences
(1407 bp in length) to see how the new Power Macs performed
relative to 030 and 040 Macs and I thought that some of the
readers of this group would be interested in the results.  
This was a heuristic search using "General" settings.  
You should remember that the
Power Macs are running in 040 emulation mode and that in
"native" mode they will be much faster if a native version
of PAUP is produced.

Machine          Runtime

IIfx             1:08
Quadra 840AV     0:27
6100/60          1:28
8100/80          1:01

These results indicate that even the fastest Power Mac
(8100/80) is barely faster in emulation mode than a
40 MHz 030 chip (IIfx) while the 6100/60 is significantly slower
than the IIfx.  The Quadra 840AV is the real peformer in
this group, over two times faster than any of the other

It is obvious that the Power Mac is not a good platform for
running PAUP unless you are using it mainly for other things
and are satisfied with IIfx-like performance.  I understand that
David Swofford is working on a Unix version of PAUP and if that
is the case, PAUP users who will be analyzing large data sets
should probably save their money and wait for that option.

Jim Manhart, Dept. of Biology, Texas A&M University, College Station, 
TX 77843-3258, (409) 845-3356, email:  J-Manhart at TAMU.EDU (Internet) 

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