Sequence Alignment by Genetic Algorithm
SAGA: Sequence Alignment by Genetic Algorithm, C. Notredame,
D.G. Higgins, Nucleic Acid Research, Vol. 24, 1515-1524, 1996.
DOWNLOADING SAGA (VERSION Updated, February 1998)
available in [ps][pdf][html].
COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
C. Notredame, L. Holme and D.G. Higgins, Bioinformatics,
Vol 14 (5) 407-422, 1998
available in [ps][pdf].
SAGA (V 0.95) is available in a TAR file, throught the following
SAGA requires a powerful UNIX station to run.
It is optimally designed for aligning less than 20 sequences,
less than 400 residues long. At present we have no plan to port it
on any non-UNIX platform. In a close future, I will support a small FAQ on
SAGA including alternative parameter setting for solving different types
of problems. Stay in touch and let me know about your needs. E-mail me any
trouble you may encounter including SAGA: BUG REPORT in your mail tiltle.
I will do my best to fix it :-).
SAGA now also includes the new COFFEE objective
function that is based on pairwise alignments consistency. As well as the
GA based optimisation, SAGA allows users to do a greedy Tree based optimisation
(T-COFFEE) that is much much much faster but less accurate....
I will keep the old version available here for
some time.... SAGA v0.93
If you wish to be informed when new updated versions will be made public,
please send me an Email firstname.lastname@example.org
including SAGA: NEW VERSION REQUEST and I will put you on my mailing
I am more than willing to help anybody who wishes to modify/improve
SAGA (i.e. insert new OFs, new mutations ....).