The G4 revolution

Mary K. Kuhner mkkuhner at kingman.genetics.washington.edu
Sat Sep 11 09:43:15 EST 1999

In article <7raral$e1h at net.bio.net>,
Hans Sluiman  <h.sluiman at rbge.org.uk> wrote:

>Obviously, existing softeware needs to be rewritten to make use of the
>new Multiprocessing and AltiVec technologies that are built into the G4.
>However, the extent to which applications will benefit from the enhanced
>FPU speed of the G4 will depend on whether they use floating point
>instructions or integers. How do PAUP et al. work?

Maximum likelihood algorithms use floating point very heavily;
anything that speeds up FP will speed up DNAML and its cousins
roughly proportionally.  Last time I profiled one of our likelihood
programs it spent over 90% of its time on FP calculations.  I 
have not looked at the PAUP* implementation but I would expect
this to be true for any ML method, since the calculations are
intrinsically FP.

I don't know if this is also true for parsimony implementations.

Mary Kuhner mkkuhner at genetics.washington.edu

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