Multiple sequence alignment in Debian.

Debian now includes many different sequence alignment programs, listed in the above table:

Program name

Licence

[http://packages.debian.org/amap-align amap]

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

[http://packages.debian.org/poa poa]

GPL

[http://packages.debian.org/probcons probcons]

public domain

[http://www.imsc.res.in/~rsidd/sigma/ sigma]

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

[http://www.biophys.uni-duesseldorf.de/stral/ stral]

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

[http://theory.med.buffalo.edu/ spem]

[http://www.biomedempire.org/ACANA ACANA]

no sources available ?

[http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html msa]

No licence found

[http://faculty.cs.tamu.edu/shsze/psalign/ psalign]

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.html SAM]

[http://www.cse.ucsc.edu/research/compbio/sam-lic/obj.0 non commercial licence]

[http://nbcr.sdsc.edu/euler/aba_v1.0/index.html aba]

[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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