[Bioperl-l] local dialign module

Jason Stajich jason at cgt.mc.duke.edu
Sun Feb 16 23:44:32 EST 2003

Mark - sounds great - we've abstrated the Clustalw implementation to be
a bit more general so hopefully it looks more like what is in the current
CVS for bioperl-run.  Specifically there is a base class that the obj
inherits from Bio::Tools::Run::WrapperBase.  Let me know if you are
confused or if you ended up writing things based on the old (1.0
bioperl) implementation.

You can submit it as a feature request through http://bugzilla.bioperl.org
and attatch the code as an attatchment.


On Sat, 15 Feb 2003, Mark Wagner wrote:

> I've written a module to run dialign2 locally (as opposed to the Pise
> remote-execution facility). I hope I didn't re-invent the wheel.
> Searching for such a module yielded no results.
> I used Bio::Tools::Run::Align::Clustalw as a basis. Basically, I
> substituted all references of clustalw with dialign2 and changed the
> parameters. Would it be worthwhile to post it to this list?

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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