[Bioperl-l] Inquiry on OrthoMCL

Aaron Mackey amackey at virginia.edu
Mon Jul 26 10:51:43 EDT 2010


OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes
sense to "wrap" it.

See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt

-Aaron

On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Hi Benard,
> Forwarding to the list for more help for you. You may want to look at the
> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live
> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to
> use this module to create an OrthoMCL wrapper. This might be more technical
> than you want. Maybe a dev on the list would be interested in creating a
> wrapper using CommandExts.
> cheers, MAJ
> ----- Original Message ----- From: "Benard Kulohoma" <
> B.Kulohoma at liverpool.ac.uk>
> To: <maj at fortinbras.us>
> Sent: Wednesday, July 21, 2010 10:58 AM
> Subject: Inquiry
>
>
> Hi Mark,
>
> I just read your bioperl resource on BWA (and here:
> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was
> most helpful. Do you have any idea of how I could use Bioperl to implement
> OrthoMCL of several bacterial genomes. I would like to find some membrane
> proteins.
>
> Many thanks,
>
> Benard
>
> PS: I am sorry for spaming/inquiring!! :)
>
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