[Bioperl-l] exonerate and crossmatch: Where are you?!

[Simon Chan]

Hey Everybody,

Awhile back, I was comparing two sequences using Ewan's pSW.pm.  I sent an email to the list because of these weird messages I was getting.  Ewan responded with:

"This is deep errors from my Wise2 package. 

I guess that you are using very very large bits of DNA that are almost
identical and that therefore Wise2 is having integer overflow problems

I would suggest switching to exonerate or crossmatch as your alignment
engine -- it will also go faster!"

source: http://bioperl.org/pipermail/bioperl-l/2002-January/007031.html

My question:  Has anyone used the above mentioned alignment engines before?  I've searched around, but had no luck.  Can someone point this lost bioperl soul in the right direction? :)

thanks, all.