Hi Torbjørn,
thanks for the clarification. Nicola, could you please comment on this?
Kind regards
Andreas.
On Tue, May 24, 2016 at 10:05:30AM +0200, Torbjørn Rognes wrote:
> Hi
>
> 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 <[email protected]> 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
>
>
--
http://fam-tille.de
