Re: (Maybe) future Debian-Med packages
> FASTA: Compares a protein sequence to another protein sequence or to a
This is Debian already, isn't it?
>
> Mummer: system for rapidly aligning entire genomes, whether in complete
> or draft form.
> Homepage: http://www.tigr.org/software/mummer/
> License: Original Artistic License (I asked upstream, since there was a
> doubt about that).
> There is a RFP open (#201761).
I kind of have packages for Mummer already. Maybe I should use the
remainder of my vacation to finish them.
> t-coffe: Multiple local sequence alignment
> Homepage:
> http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
> License: Academic License (???)
> 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.
> wise2: package that is focused on comparing DNA sequences at the level
> of its conceptual translation, regardless of sequencing error and introns.
> Homepage: http://www.ebi.ac.uk/Wise2/
> License: GNU GPL
> 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.
> Smile: Find statistically significant patterns in sequences
> Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
> License: GNU GPL
> Debian package available at http://tp12.pzr.uni-rostock.de/~moeller/debian/
> Open ITP (#221492).
It is mine. Upstream just incorporated the licenses and I probably come
up with the package very soonish.
A very nice package to have would be SSAHA, which is distributed in the
same CVS as Wise2, performing DNA/DNA similarity searches.
Many greetings
Steffen
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