Re: (Maybe) future Debian-Med packages
Hi
> > FASTA: Compares a protein sequence to another protein sequence or to a
> This is Debian already, isn't it?
Hum... I didn´t find it.
$ apt-cache search fasta
seaview - [Biology] A multiple sequence alignment editor
clustalw - [Biology] Global multiple nucleotide or peptide sequence alignment
t-coffee - local multiple DNA and protein sequence alignment
Neither on WNPP I found.
> > t-coffe: Multiple local sequence alignment
> > There is an open ITP with more than 1 year (#205370). I have talked to
> It is my ITP, I presume. My package is ready, it is only upstream
> specifying the license that I was waiting for and then forgot to remind.
> There are now other alignment programs out that compete nicely with
> Clustal and T-Coffee. Good to hear GPL to be coming, soon. T-Coffee
> shares some source with Clustalw, the latter being in non-free, so we
> need to wait for more than an inofficial "it's ok", I suggest, before
> going forward with the packaging.
Cedric Notredame <cedric.notredame@igs.cnrs-mrs.fr> said:
My policy is to not prevent anyone from doing anything and the next t_coffee
distribution will be freeware under an open GPL licence. This being said,
please be aware that the code is being actively developped these days and
that you may need some automatic mecanism to check for updates (there is
such a flag in the latest distribution : -update that returns the latest
version).
So, the correct is to wait, as you said.
> > wise2: package that is focused on comparing DNA sequences at the level
> > There is a RFP open (#200591).
> And an ITP of mine. wise2 is a beast, as recent versions require the
> existance of earlier versions to compile dynamite. Args. It would be
> great if you could do this one. Please be aware that the latest source
> is distributed in CVS only. 2.2 did not have this constraint and could
> possibly be used for the bootstrap.
Yes. But the bug #200591 was retitled to RFP. It would be good if ypu change back to ITP.
> A very nice package to have would be SSAHA, which is distributed in the
> same CVS as Wise2, performing DNA/DNA similarity searches.
You could package SSAHA too, if possible, since you have familiarity with Wise2.
And sorry if I passed an image that I was trying to "steal" your packages. It is not what I want. I had just created a list with the packages that I thought would be useful ;-)
Cheers
Nelson
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