[BiO BB] BALiBASE is a benchmark for alignment procedures

Dr. Christoph Gille christoph.gille at charite.de
Tue Dec 20 14:04:05 EST 2005

The performance of different sequence alignment methods can be
assessed using BALiBASE.  I have embedded BALiBASE in STRAP and
started to compute a table of score values for different alignment
procedures:ClustalW, Mafft5,T_Coffee, Muscle, Align_m, Dialign2,
DialignT, Probcons2, MultiAlignerNeoBio, JAligner


Using the GUI it is very simple to compute a table for any set of
alignment methods.  But it takes quite a lot of time (~ 48h ) and the entire
table is not finished yet.

Computation is performed with default parameters for all alignment
methods.  NeoBio and JAligner are pair alignment methods and had been
turned into multiple sequence alignment methods using a very primitive
approach. So it is not completely fair to compare them to those that
are primarily multiple sequence aligners.

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