[Bioperl-l] Purge command in SimpleAlign

[jrest@umich.edu]

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?)

Thanks!
Josh