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Revision 27 as of 2009-03-16 03:36:23
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||[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://dialign-t.gobics.de/ dialign-t] ||LGPL ||○ ||○ ||
||[http://packages.debian.org/kalign kalign] ||GPL || ||○ ||
||[http://align.bmr.kyushu-u.ac.jp/mafft/software/ mafft] ||BSD ||○ ||○ ||
||[http://packages.debian.org/muscle muscle] ||Public domain ||○ ||○ ||
||[http://packages.debian.org/poa poa] ||GPL ||○ ||○ ||
||[http://packages.debian.org/probcons probcons] ||public domain ||○ ||○ ||
||[http://packages.debian.org/proda proda] ||public domain || || ||
||
[http://www.imsc.res.in/~rsidd/sigma/ sigma] ||GPL || || ||
||[http://packages.debian.org/t-coffee t-coffee] ||GPL ||○ ||○ ||
||[[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://dialign-t.gobics.de/|dialign-t]] ||LGPL ||○ ||○ ||
||[[http://packages.debian.org/kalign|kalign]] ||GPL || ||○ ||
||[[http://align.bmr.kyushu-u.ac.jp/mafft/software/|mafft]] ||BSD ||○ ||○ ||
||[[http://packages.debian.org/muscle|muscle]] ||Public domain ||○ ||○ ||
||[[http://packages.debian.org/poa|poa]] ||GPL ||○ ||○ ||
||[[http://packages.debian.org/probcons|probcons]] ||public domain ||○ ||○ ||
||[[http://packages.debian.org/proda|proda]] ||public domain || || ||
||[
[http://www.imsc.res.in/~rsidd/sigma/|sigma]] ||GPL || || ||
||[[http://packages.debian.org/t-coffee|t-coffee]] ||GPL ||○ ||○ ||
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There are summaries available about the programs [http://qa.debian.org/developer.php?packages=amap-align+clustalw+dialign+kalign+muscle+poa+probcons+proda+sigma-align+t-coffee version numbers] as well as their [http://people.debian.org/~igloo/popcon-graphs/index.php?packages=kalign+dialign+probcons+proda+clustalx+clustalw+muscle+t-coffee+poa+amap-align+sigma-align&show_installed=on&want_legend=on&beenhere=1 popularity] in Debian. There are summaries available about the programs [[http://qa.debian.org/developer.php?packages=amap-align+clustalw+dialign+kalign+muscle+poa+probcons+proda+sigma-align+t-coffee|version numbers]] as well as their [[http://people.debian.org/~igloo/popcon-graphs/index.php?packages=kalign+dialign+probcons+proda+clustalx+clustalw+muscle+t-coffee+poa+amap-align+sigma-align&show_installed=on&want_legend=on&beenhere=1|popularity]] in Debian.
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Most of the above packages have been benchmarked on protein sequences by [http://www.biomedcentral.com/1741-7007/4/41 Nuin, Wang & Tillier]. Most of the above packages have been benchmarked on protein sequences by [[http://www.biomedcentral.com/1741-7007/4/41|Nuin, Wang & Tillier]].
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||[http://evol-linux1.ulb.ac.be/ueg/ProAlign/ ProAlign] ||GPL || ||[[http://evol-linux1.ulb.ac.be/ueg/ProAlign/|ProAlign]] ||GPL ||
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||[http://foldalign.ku.dk/software/index.html FoldalignM] ||GPL ||Depends on java... ||
||[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://prodata.swmed.edu/mummals/mummals.php MUMMALS] ||unknown ||Enquiring about the licence ||
||[http://www.biophys.uni-duesseldorf.de/stral/ stral] ||GPL ||depends on the "Vienna RNA package", which is non-free and not yet packaged ||
||[http://treerefiner.stanford.edu/download.html treefinder] ||Public domain ||please submit an RFP to fast-track this pacakage if you want ||
||[http://ai.stanford.edu/~flannick/typhon/ typhon] ||Public domain ||please submit an RFP to fast-track this pacakage if you want ||
||[[http://foldalign.ku.dk/software/index.html|FoldalignM]] ||GPL ||Depends on java... ||
||[[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://prodata.swmed.edu/mummals/mummals.php|MUMMALS]] ||unknown ||Enquiring about the licence ||
||[[http://www.biophys.uni-duesseldorf.de/stral/|stral]] ||GPL ||depends on the "Vienna RNA package", which is non-free and not yet packaged ||
||[[http://treerefiner.stanford.edu/download.html|treefinder]] ||Public domain ||please submit an RFP to fast-track this pacakage if you want ||
||[[http://ai.stanford.edu/~flannick/typhon/|typhon]] ||Public domain ||please submit an RFP to fast-track this pacakage if you want ||
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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. 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.
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||[http://research.amnh.org/scicomp/projects/malign.php malign] ||unclear (discrepancies between files) || ||[[http://research.amnh.org/scicomp/projects/malign.php|malign]] ||unclear (discrepancies between files) ||
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||[http://theory.med.buffalo.edu/ spem] || ||
||[http://www.bx.psu.edu/projects/esperr/ ESPERR] ||Licence not found ||
||[http://www.biomedempire.org/ACANA ACANA] ||no sources available ? ||
||[http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html msa] ||No licence found ||
||[http://bibiserv.techfak.uni-bielefeld.de/dca/ dca]||No license 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 ||
||[ftp://iole.swmed.edu/pub/PCMA/ PCMA] ||no profit ||
||[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] ||
||[http://www.drive5.com/lobster/index.htm SATCHMO] ||[http://www.drive5.com/lobster/license.htm Licence] does not allow redistribution, superseded by muscle ||
||[[http://theory.med.buffalo.edu/|spem]] || ||
||[[http://www.bx.psu.edu/projects/esperr/|ESPERR]] ||Licence not found ||
||[[http://www.biomedempire.org/ACANA|ACANA]] ||no sources available ? ||
||[[http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html|msa]] ||No licence found ||
||[[http://bibiserv.techfak.uni-bielefeld.de/dca/|dca]]||No license 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 ||
||[[ftp://iole.swmed.edu/pub/PCMA/|PCMA]] ||no profit ||
||[[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]] ||
||[[http://www.drive5.com/lobster/index.htm|SATCHMO]] ||[[http://www.drive5.com/lobster/license.htm|Licence]] does not allow redistribution, superseded by muscle ||
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 Back to ["DebianScience/Biology"]  Back to [[DebianScience/Biology]]

Multiple sequence alignment in Debian.

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

Program name

Licence

M-Coffee

DM-Coffee

amap

public domain

clustalw

No modification, no for-profit use without authorisation (see licence)

dialign

LGPL

dialign-t

LGPL

kalign

GPL

mafft

BSD

muscle

Public domain

poa

GPL

probcons

public domain

proda

public domain

sigma

GPL

t-coffee

GPL

M-Coffee and DM-Coffee are special modes of the t_coffee program, which align the sequence using diverse programs, and combine their outputs into a better alignment. DM-Coffee uses only free software.

There are summaries available about the programs version numbers as well as their popularity in Debian.

Most of the above packages have been benchmarked on protein sequences by Nuin, Wang & Tillier.

Scheduled for packaging

An Intend To Package bug has been reported for the following package:

Program name

Licence

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

FoldalignM

GPL

Depends on java...

Handel

GPL

part of the dart package, which does not build out of the box on powerpc

MUMMALS

unknown

Enquiring about the licence

stral

GPL

depends on the "Vienna RNA package", which is non-free and not yet packaged

treefinder

Public domain

please submit an RFP to fast-track this pacakage if you want

typhon

Public domain

please submit an RFP to fast-track this pacakage if you want

Non-free, non-packaged software

The following programs do not meet the 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 ?

prrn

no profit

malign

unclear (discrepancies between files)

saga

non-redistributable

spem

ESPERR

Licence not found

ACANA

no sources available ?

msa

No licence found

dca

No license found

psalign

No licence found

BlastAlign

no licence found

marna

no licence found

PCMA

no profit

SAM

non commercial licence

aba

no redistribution, no profit

SATCHMO

Licence does not allow redistribution, superseded by muscle

See also

Wikipedia has a nice page summarising the multiple alignment softwares: http://en.wikipedia.org/wiki/Sequence_alignment_software