[Inparanoid] Analyzing 17 proteome orthology with Inparanoid

Sammy Desilva sammy.ich17 at gmail.com
Tue Oct 7 13:27:56 CEST 2014


Dear Prof. Sonnhammer,

I understand in case of 17 proteome I have to use multiparanoid for
clustering after computing 17*16/2 = 136 pairs with InParanoid. I wonder is
any script already available to automate the computations of multiple pairs
(here 136) with InParanoid for getting input for MultiParanoid?

Regads
Sammy


On Mon, Sep 22, 2014 at 2:33 PM, Erik Sonnhammer <
erik.sonnhammer at scilifelab.se> wrote:

>  Hi,
>
> If you want ortholog groups that include all 17 species, InParanoid won't
> work. But if you only need pairwise relationships (which is usually the
> case) then it will.  Then you have to run InParanoid for all 17*16/2 pairs.
>
> Erik Sonnhammer
>
> On 09/20/2014 11:32 AM, Sammy Desilva wrote:
>
>  Hi, I want to assign orthology relationship among 17 proteomes. Could
> someone please suggest me how to do it offline in Inparanoid? The running
> command for such cases? I guess putting 3 organism it treats third as
> outgroup.
>  Thanks
>
>
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>
>
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