[Primeusers] PrimeGSR memory usage

[Filipe Garrett]

Dear Lars,

As I had already told you, I am working with two datasets: one with 90 and the other with 375 sequences.
With the smallest one I have no problem when I use a scaled tree to a root of 1.0 but, with the 
other, even with the scaled tree, I have to increase the "-c" option a lot.
While the first dataset works with a "-c 90", the second needs at least a "-c 650"! I've only tried 
until "-c 650" since, at these level, primeGSR already uses over 33Gb of memory and still outputs 
the error message:

"
Error:
       Probability: Division with zero attempted!
"


Is this normal and is there a way to reduce memory usage?
Does the quality of the alignment has any influence in running time and memory usage? Does the 
alignment quality has a great influence on the birth and death rates estimates? I'm asking these 
because I'm working with a rather divergent gene family and the alignment is likely to have a lot of 
gaps (automatic alignment with no manual revision). I'm mainly interested on the birth and death 
rates estimates...

thanks for your time,
FG

-- 
Filipe G. Vieira
Departament de Genetica
Universitat de Barcelona
Av. Diagonal, 645
08028 Barcelona
SPAIN
Phone: +34 934 035 306
Fax: +34 934 034 420
fgarret at ub.edu
http://www.ub.edu/molevol/