[Bioperl-l] Bio:: namespace question

Jason Stajich jason.stajich at duke.edu
Sat Jul 30 12:28:37 EDT 2005

You'll see there are other non-bioperl modules in CPAN under the Bio:: 
namespace so we haven't got any reservations on what people can submit 
to CPAN.  We have some phylogenetics related modules scattered in 
bioperl to logically deal with data parsing mostly (Bio::Tree, 
Bio::TreeIO, Bio::Tools::Phylo) and running (Bio::Tools::Run::Phylo).

My concern is mostly with confusing people about how things interrelate 
and can be used together and not having a namespace clash, but we are 
not currently using Bio::Phylo.

I don't know if any other folks have opinions -- I suppose waiting to 
see what I'd say?


On Jul 30, 2005, at 7:01 AM, Rutger Vos wrote:

> Dear fellow perl-using-biologists,
> I want to submit to CPAN a module for phylogenetic analysis. I am 
> trying to decide what top-level namespace to use. Can I use Bio::Phylo 
> or something like that? Or is Bio:: reserved for BioPerl?
> Thanks!
> Rutger
> -- 
> ++++++++++++++++++++++++++++++++++++++++++++
> Rutger Vos, PhD. candidate
> Department of Biological Sciences
> Simon Fraser University
> 8888 University Drive
> Burnaby, BC, V5A1S6
> Phone: 604-291-5625 Fax: 604-291-3496
> Personal site: http://www.sfu.ca/~rvosa
> FAB* lab: http://www.sfu.ca/~fabstar
> ++++++++++++++++++++++++++++++++++++++++++++
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Jason Stajich
jason.stajich -at- duke.edu

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