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://barton.ebi.ac.uk/servers/amas_server.html
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://bips.u-strasbg.fr/fr/Documentation/ClustalX/
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.fundp.ac.be/sciences/biologie/bms/matchbox_submit.shtml
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/tools/#align).

Abbreviation: MSA, multiple sequence alignment.

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

Last update: 28 January, 2010