Re: Debian packaging of phylophlan and using vsearch instead of usearch

Hi Adreas,

we recently updated PhyloPhlAn to support other usearch versions. I'm CC'ing Francesco (the lead on the project) which can be more accurate on which usearch version we need for the last version of PhyloPhlAn.

Regarding other software I think it would be fantastic to have MetaPhlAn2 as a Debian package. It's here: https://bitbucket.org/biobakery/metaphlan2 . It is widely used and stable (although we are further and actively developing it) and published a couple of times in Nat Methods.

Another software we developed that would be great to have as a Debian package is GraPhlAn (https://bitbucket.org/nsegata/graphlan/wiki/Home) (Described here https://peerj.com/articles/1029/). It's a package to produce nice graphical representation of phylogenetic trees.

Importantly, these two packages don't use any proprietary software so it should be easier to package them than PhyloPhlAn.

Let us know if you have any question and if we can help you somehow!

thanks

Nicola

On Wed, May 25, 2016 at 7:49 AM Andreas Tille <andreas@an3as.eu> wrote:

Hi Nicola,

thanks for your reply.

On Tue, May 24, 2016 at 07:06:54PM +0000, Nicola Segata wrote:
> Hi Torbjørn and Andreas,
> yes, as Torbjørn said we indeed need to use translated search for
> PhyloPhlAn and that's the reason why we cannot substitute usearch with
> vsearch (as we instead happily did for other software we developed).

Thanks for confirming Torbjørn's assumption. I have two further
questions:
1. PhyloPhlAn wiki talks about version 5 of userach and version 6 is
not supported. However usearch is now et version 8. Is it correct
that our users need to download usearch 5 if they want to use
PhyloPhlAn?
2. If you are talking about other software: Can you imagine other
targets for Debian packaging from your software pool?

Kind regards

Andreas.

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