Web document 6.8. Summary of multiple sequence alignment resources available on the internet.

 

 

Program

Description, URL

AMAS (Analyse Multiply Aligned Sequences)

At the European Bioinformatics Institute; used to analyze premade MSAs

http://www.compbio.dundee.ac.uk/www-amas/

CINEMA

Colour INteractive Editor for Multiple Alignments

► http://utopia.cs.manchester.ac.uk/

ClustalW

At the European Bioinformatics Institute and other sites

► http://www.ebi.ac.uk/clustalw/

ClustalX

Download by FTP

►http://www.clustal.org/

DIALIGN

Especially useful for local MSA; from the University of Bielefeld, Germany

► http://bibiserv.techfak.uni-bielefeld.de/dialign/

Match-Box Web Server 1.3

From the University of Namur, Belgium

►http://www.unamur.be/sciences/biologie/urbm/bioinfo/matchbox/

MultAlin

From INRA (http://www.inra.fr/), Toulouse

► http://bioinfo.genopole-toulouse.prd.fr/multalin/multalin.html

Multiple Sequence Alignment version 2.0

At the GeneStream server of the Institut de Génétique Humaine

► http://xylian.igh.cnrs.fr/msa/msa.html

Musca

From the IBM Bioinformatics Group

► http://cbcsrv.watson.ibm.com/Tmsa.html

PileUp

Commercial package available through the SeqWeb or UNIX versions of the Genetics Computer Group (GCG)

► http://www.accelrys.com/products/gcg/

T-COFFEE

Slower but more accurate than ClustalW for distantly related proteins

► http://www.tcoffee.org/

 

Note: Additional algorithms are listed at ExPASy (http://www.expasy.org/genomics/sequence_alignment).

 

Abbreviation: MSA, multiple sequence alignment.

Please let me know about broken links, or suggest links to add (email here).

Last update: 28 January, 2010