[Bioperl-l] Performance of Bio::Species

Sendu Bala bix at sendu.me.uk
Tue Nov 21 14:37:14 EST 2006


Stefan Kirov wrote:
> New Bio::Species implementation seems to degrade significantly 
> performance. It seems this happens when the Bio::Tree::Tree is constructed.
> See the stats bellow (based on simple Bio::Species object construction, 
> script and test sequence file attached):
[snip]

Thanks. If you come up with anything, please file that bug report. I 
certainly regard this as an important thing that must be fixed, though I 
don't know if I should hold up release of 1.5.2 for it. Now that you've 
reported on it I'm leaning toward yes, since the new Bio::Species 
implementation is one of the major new features of 1.5.2 and it ought to 
work well.

Anyway, for the memory leak I have some ideas I haven't tried yet; I 
don't know if my efforts will solve the speed issue though.

If anyone can spare the time to look at the problem, please do.


Cheers,
Sendu.


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