The Need for Speed

Julian julian.robinson at plant-sciences.oxford.ac.uk
Fri Sep 17 10:21:45 EST 1999

[**see Moderator's note below before attempting post attachments**]

> The PHYLIP documentation has such benchmarks for some older machines;
> you could pick up the two data sets (a "best case" data set with
> very high information content, and a "worst case" noisy one) used
> for that, and get a bunch of early-machine benchmarks for comparison.
> Mary Kuhner mkkuhner at genetics.washington.edu

Yes, this is along the line of what I had in mind.
Two data sets, one 'messy' and one 'clean'.
The problem here is the extent of 'messiness',
we want to able to complete the search. I have a set of
sequences, but PAUP runs out of memory @18,000 trees.
I have a  'clean' data set, but this is only due to a lack of
variable characters.

What I would like to do is post both data sets to the newsgroup (see below),
hopefully some people will run them for us, and I can gather a list of
Machine types
(is PAUP* 4.0 quicker on IBM or MAC, what about Mainframe UNIX machines),
'clock speed' , operating system (e.g. Mac OS 7.5.5 -vs- Mac OS 8.5, etc..),
and how fast the search was completed.
We should also do this for other searches in PAUP such a ml, etc. and for

Posting data sets.- I know some newsgroups are not very keen on 'binaries'
being posted,
mainly due to problems people have downloading data from their ISPs (i.e.
they are on the phone longer),
but this group I guess is mainly academic and we don't have to pay for our
internet access.
The alternative is to get in contact with me directly, and I we can go from
there in devising some
sort of strategy.

Dr. J Robinson,
Dept. of Plant Sciences,
University of Oxford.
e-mail: julian.robinson at plants.ox.ac.uk
tel: 01865-275020.

Moderator's note: Please do not try to post attachments (whether
binaries or ASCII text). I am not able to forward the attachments for
posting. If you want to post datasets for benchmarking in this newsgroup,
post them as in the ordinary message body. Or contact Julian Robinson
directly (julian.robinson at plants.ox.ac.uk). 


Jerry Learn
<learn at u.washington.edu>

co-moderator of bionet.molbio.evolution 

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