Table 4. Sequence Alignment Programs and Resources
Servers for Aligning Two Sequences
Program Website Comments
Align http://genome.cs.mtu.edu/align.html Multiple methods. Excellent for aligning DNA
Lalign http://www.ch.embnet.org/software/LALIGN_form.html Finds multiple matching subsegments in two sequences
FASTA http://fasta.bioch.virginia.edu/ Useful for accurate alignment of DNA
Alion http://fold.stanford.edu/alion/ Aligns two protein sequences (global or local alignment)
bl2seq http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html Aligns two sequences using BLAST. Very quick
Servers for Pairwise Alignment of Multiple Sequences
Program Website Comments
Muscle http://www.bioinformatics.nl/tools/muscle.html High accuracy and ultra fast. Outperforms Clustalw
Muscle http://http://www.drive5.com/muscle/.html Outperfomrs Clustalw. Limited on server to 200 sequences
ClustalW http://www.ebi.ac.uk/clustalw/index.html General purpose, fast, handles many sequences
ClustalW http://www.ch.embnet.org/software/ClustalW.html Limited to 30 sequences
ClustalW http://services.bioasp.nl/blast/cgi-bin/clustal.cgi Associated with phylogenetic trees
ClustalW http://www.ddbj.nig.ac.jp/E-mail/clustalw-e.html Associated with phylogenetic trees
T-Coffee http://igs-server.cnrs-mrs.fr/Tcoffee/ Structure-based alignments. Limited to 50 sequences.
T-Coffee http://www.ch.embnet.org/software/TCoffee.html Good for divergent sequences. Limited to 30 sequences
BCM http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html Multiple methods (progressive & pattern-based)
Alignment Editing, Analyses and Shading/Printing Tools
Program Website Comments
MatchBox http://www.sciences.fundp.ac.be/biologie/bms/help.html




 
Finding & aligning conserved segments. No gap penalties
MEME http://meme.sdsc.edu/meme/website/meme.html Motif discovery in a group of related sequences
Gibbs http://bayesweb.wadsworth.org/gibbs/gibbs.html Motif discovery in a group of related sequences
Dialign http://bibiserv.techfak.uni-bielefeld.de/dialign/ Finds local similarities among distantly related sequences
BlockMaker http://blocks.fhcrc.org/make_blocks.html Motif discovery in a group of related sequences
Servers for Aligning Two Sequences
Program Website Comments
ClustalX1 http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html Pairwise alignment program for local installation
Jalview http://www.jalview.org/ Alignment editor and viewer for local installation
Genedoc http://www.psc.edu/biomed/genedoc/ Alignment editor and viewer for local installation
Boxshade http://www.ch.embnet.org/software/BOX_form.html Pretty printing and shading
Weblogo http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi Generates sequence logos
Blocks http://blocks.fhcrc.org/blocks/process_blocks.html Generates sequence logos
1) Graphical interface for ClustalW. The version for Mac (OS-X) is available at http://www.embl-heidelberg.de/~chenna/clustal/darwin/.