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


I am not sure exactly how phylophlan works, but it seems like it is based on amino acid sequences.

In contrast to usearch, vsearch does not handle amino acid sequences, only nucleotide sequences. We do not have any plans to include support in vsearch for amino acid sequences in the near future.

It thus appears that vsearch would unfortunately not be a useful alternative to usearch in this case.

Best wishes,

- Torbjørn

> On 23 May 2016, at 18:17, Andreas Tille <andreas@an3as.eu> wrote:
> Hi Nicola,
> I'm writing to you on behalf of the Debian Med team which is a group
> inside Debian that intends to package Free Software in the field of
> biology and medicine for main Debian.  I received a user request to
> package phylophlan and have created some packaging code[1].
> The packaging involved some tweaking since the code belongs to
> /usr/share/phylophlan since it is not changable while the data need to
> be unpackaged (and thus written by users) and so were moved to
> /var/lib/phylophlan.  This patch[1] is not a big deal and could remain
> for the Debian packaging exclusively.
> However, there is a problem with usearch.  We can not package this tool
> for Debian since it is non-free and we are not allowed to build it from
> source.  The good news is that there is a free replacement vsearch[3].
> So I tried to create a patch to use vsearch instead of usearch[4].  When
> doing so I learned that both tools are not compatible regarding command
> line options and phylophlan might need some better adaption than the
> very simple patch[4] I used.
> Before I'd dive more into the details I'd like to know whether you would
> be interested in supporting vsearch in parallel to usearch in phylophlan
> or whether you leave us on our own with developing and maintaining the
> patch.
> Kind regards and thanks for providing phylophlan as free software
>     Andreas.
> [1] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/
> [2] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/debian/patches/datadir.patch?revision=22007&view=markup
> [3] https://github.com/torognes/vsearch/
> [4] https://anonscm.debian.org/viewvc/debian-med/trunk/packages/phylophlan/trunk/debian/patches/use_vsearch.patch?view=markup
> -- 
> http://fam-tille.de

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