OT processes and cpu use

[Tyler Smith <tyler.smith@mail.mcgill.ca>]

Hi,

I have a general question about processes in GNU/Linux. I'm working
with PAUP, which is a command-line tool for calculating phylogenies
from various data types (gene sequencies, proteins etc.). This sort of
analysis routinely takes hours to days of processing. I find it is
convenient to run paup in *shell* mode inside emacs -nw, allowing me to
easily yank commands from various files into the paup process.

When I check with top, it appears that paup is using 99% of the CPU
when I do this, which is as it should be. I just wanted to check with
more experienced people to verify that running paup from within emacs
is not going to incur a performance hit. The analysis I have running
at the moment (heuristic search) will take more than 5 hours, and if
that works properly I'll be continuing on with a follow-up (bootstrap)
that will take several days, so tweaking performance is a non-trivial
concern.

Any comments on my current set-up or suggestions for ways to tweak
performance in any way would be most welcome!

-- 
Regards,

Tyler Smith