[Bioperl-l] Purge command in SimpleAlign

[Ewan Birney]

On Thu, 20 Dec 2001 jrest@umich.edu wrote:

> Concerning the purge function in SimpleAlign:
> 
> "Function: removes sequences above whatever %id"
> "This function will grind on large alignments. Beware!"
> "(perhaps not ideally implemented)"
> 
> This is true!  It worked great with 10, but with 40,000 sequences, it 
> "grinds."
> 
> Is there an alternative method someone can suggest to implement this 
> function?  Are there any other pieces of code or software (perl or 
> otherwise) to implement a "purge" (beside blast?)

You could also look at writing a better method - should be ok - just need
to linearise the main loop rather than it being the square of the number
of sequences. 




> 
> Thanks!
> Josh
> 
> 
> 
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