Consensus from Multiple Alignments

Anders Gorm Pedersen gorm at
Wed Nov 1 07:40:23 EST 2000

Tim Spahlinger wrote:

> Can somebody recommend a web site (preferred) or a software
> package (I'd rather save my limited funding) that will give
> me a consensus sequence of bases derived from the multiple
> alignments of several sequences? 


Call me a puritan, but I would warn against using consensus sequences for most
purposes (most of the information contained in the alignment is thrown away, a
consensus sequence is not necessarily represented even once in the original data
set, etc., etc.). 

A very informative alternative is a sequence logo. An online server is available

More info on logos:

More info on information theory:

Best regards,
Anders Gorm Pedersen

 Anders Gorm Pedersen, cand.scient., Ph.D.  (gorm at

 Center for Biological Sequence Analysis
 Technical University of Denmark
 Bldg 208, DK-2800 Lyngby, Denmark

 phone: (+45) 45 25 24 84
 fax:   (+45) 45 93 15 85


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