Multiple sequence alignment in Debian.
Debian now includes many different sequence alignment programs, listed in the above table:
Program name |
Licence |
public domain |
|
[http://packages.debian.org/clustalw clustalw] |
No modification, no for-profit use without authorisation (see [http://packages.debian.org/changelogs/pool/non-free/c/clustalw/clustalw_1.83-1/clustalw.copyright licence]) |
[http://packages.debian.org/dialign dialign] |
LGPL |
[http://packages.debian.org/kalign kalign] |
GPL |
[http://packages.debian.org/muscle muscle] |
Public domain |
GPL |
|
[http://packages.debian.org/probcons probcons] |
public domain |
GPL |
|
[http://packages.debian.org/t-coffee t-coffee] |
GPL |
Scheduled for packaging
An Intend To Package bug has been reported for the following package:
Program name |
Licence |
[http://evol-linux1.ulb.ac.be/ueg/ProAlign/ ?ProAlign] |
GPL |
Not yet scheduled for packaging
The following packages could be distributed in Debian, and maybe will be in the future. You can help us to make this happening faster by joining the DebianMed team!
Program name |
Licence |
Notes about packaging |
[http://dialign-t.gobics.de/ dialign-t] |
LGPL |
makefile is specific to ia32 |
[http://biowiki.org/HandelPackage Handel] |
GPL |
part of the [http://sourceforge.net/projects/dart dart] package, which does not build out of the box on powerpc |
GPL |
depends on the "Vienna RNA package", which is non-free and not yet packaged |
Non-free, non-packaged software
The following programs do not meet the [http://www.debian.org/social_contract#guidelines Debian Free Software Guidelines]: they restrict usage (non-profit), they do not allow the redistribution of the sources, or do not make them available at all. These programs will not be packaged unless requested. Non-free programs are more difficult to manage, for instance charging money for the shippment of a CD-ROM containing software is a for-profit use, which makes necessary to ask for many exemptions to the copyright holders. Nevertheless, if you need one of these programs packaged for Debian, please contact us on the mailing list of the DebianMed project.
Program name |
Why is it not packaged ? |
mafft |
no profit |
prrn |
no profit |
[http://research.amnh.org/scicomp/projects/malign.php malign] |
unclear (discrepancies between files) |
saga |
non-redistributable |
|
|
no sources available ? |
|
[http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html msa] |
No licence found |
No licence found |
|
[http://evolve.zoo.ox.ac.uk/software.html?id=blastalign ?BlastAlign] |
no licence found |
[http://www.bio.inf.uni-jena.de/Software/MARNA/index.html marna] |
no licence found |
[http://www.cse.ucsc.edu/research/compbio/sam-lic/obj.0 non commercial licence] |
|
[https://nbcr.sdsc.edu/euler/RegDownload/cgi-bin/aba_v1.0-reg.cgi no redistribution, no profit] |
See also
Wikipedia has a nice page summarising the multiple alignment softwares: http://en.wikipedia.org/wiki/Sequence_alignment_software
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