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

Currently there is not plan to package new programs for multiple sequence alignment. But suggestions and requests are most welcome, on the DebianMed discussion list.

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

ProAlign

GPL

No build system found

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