List of sequence alignment software

This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.

Database search only

Name	Description	Sequence Type*	Link
BLAST	k-tuple local search (Basic Local Alignment Search Tool)	Both	NCBI EBI DDBJ DDBJ (psi-blast) GenomeNet PIR (protein only)
Combinatorial Extension	Structural alignment search	Protein	server
FASTA	k-tuple local search	Both	EBI DDBJ GenomeNet PIR (protein only)
GGSEARCH / GLSEARCH	Global:Global (GG), Global:Local (GL) alignment with statistics	Protein	FASTA server
HMMER	Hidden Markov profile search	Protein/DNA	download (S. Eddy) DDBJ (HMMPFAM)
IDF	Inverse Document Frequency	Both	Download
Infernal	profile SCFG search	RNA	download (S. Eddy)
SAM	Hidden Markov profile search	Protein/DNA	SAM (K. Karplus, A. Krogh)
SSEARCH	Smith-Waterman search (more sensitive than FASTA)	Both	EBI DDBJ server
*Sequence Type: Protein or nucleotide

Pairwise alignment

Name	Description	Sequence Type*	Alignment Type**	Link	Author	Year
BLASTZ	Seeded pattern-matching	Nucleotide	Local	download	Schwartz et al.	2003
DNADot	Web-based dot-plot tool	Nucleotide	Global	server	R. Bowen	1998
DOTLET	Java-based dot-plot tool	Both	Global	applet	M. Pagni and T. Junier	1998
GGSEARCH, GLSEARCH	Global:Global (GG), Global:Local (GL) alignment with statistics	Protein	Global in query	FASTA server	W. Pearson	2007
JAligner	Open source Java implementation of Smith-Waterman	Both	Local	JWS	A. Moustafa	2005
LALIGN	Multiple, non-overlapping, local similarity (same algorithm as SIM)	Both	Local non-overlapping	server FASTA server	W. Pearson	1991 (algorithm)
matcher	Memory-optimized needleman but slow dynamic programming (based on LALIGN)	Both	Local	server	I. Longden (modified from W. Pearson)	1999
MCALIGN2	explicit models of indel evolution	DNA	Global	server	J. Wang et al.	2006
MUMmer	Suffix-Tree based	Nucleotide	Global	download	S. Kurtz et al.	2004
needle	Needleman-Wunsch dynamic programming	Both	Global	server	A. Bleasby	1999
Ngila	logarithmic and affine gap costs and explicit models of indel evolution	Both	Global	download	R. Cartwright	2007
PatternHunter	Seeded pattern-matching	Nucleotide	Local	download	B. Ma et al.	2002-2004
ProbA (also propA)	Stochastic partition function sampling via dynamic programming	Both	Global	download	U. Mückstein	2002
PyMOL	"align" command aligns sequence & applies it to structure	Protein	Global (by selection)	site	W. L. DeLano	2007
REPuter	Suffix-Tree based	Nucleotide	Local	download	S. Kurtz et al.	2001
SEQALN	Various dynamic programming	Both	Local or Global	server	M.S. Waterman and P. Hardy	1996
SIM, GAP, NAP, LAP	Local similarity with varying gap treatments	Both	Local or global	server	X. Huang and W. Miller	1990-6
SIM	Local similarity	Both	Local	servers	X. Huang and W. Miller	1991
SLIM Search	Ultra-fast blocked alignment	Both	Both	site	L. Bloksberg	2004
SSEARCH	Local (Smith-Waterman) alignment with statistics	Protein	Local	FASTA server	W. Pearson	1981 (Algorithm)
stretcher	Memory-optimized but slow dynamic programming	Both	Global	server	I. Longden (modified from G. Myers and W. Miller)	1999
tranalign	Aligns nucleic acid sequences given a protein alignment	Nucleotide	NA	server	G. Williams (modified from B. Pearson)	2002
water	Smith-Waterman dynamic programming	Both	Local	server	A. Bleasby	1999
wordmatch	k-tuple pairwise match	Both	NA	server	I. Longden	1998
YASS	Seeded pattern-matching	Nucleotide	Local	server download	L. Noe and G. Kucherov	2003-2006
BioPerl dpAlign	dynamic programming	Both	Both + Ends-free	site	Y. M. Chan	2003
*Sequence Type: Protein or nucleotide. **Alignment Type: Local or global

Multiple sequence alignment

Name	Description	Sequence Type*	Alignment Type**	Link	Author	Year
ABA	A-Bruijn alignment	Protein	Global	download	B.Raphaelet al.	2004
ALE	manual alignment ; some software assistance	Nucleotides	Local	download	J. Blandy and K. Fogel	1994 (latest version 2007)
AMAP	Sequence annealing	Both	Global	server	A. Schwartz and L. Pachter	2006
BAli-Phy	Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation	Both	Global	WWW+download	BD Redelings and MA Suchard	2005 (latest version 2007)
CHAOS/DIALIGN	Iterative alignment	Both	Local (preferred)	server	M. Brudno and B. Morgenstern	2003
ClustalW	Progressive alignment	Both	Local or Global	download EBI DDBJ PBIL EMBNet GenomeNet	Thompson et al.	1994
CodonCode Aligner	Multi alignment; ClustalW & Phrap support	Nucleotides	Local or Global	download	P. Richterich et al.	2003 (latest version 2007)
DIALIGN-TX and DIALIGN-T	Segment-based method	Both	Local (preferred) or Global	download and server	A.R.Subramanian	2005 (latest version 2008)
DNA Baser	Multi alignment	Both	Local or Global + Post processing	DNA Baser (commercial)	M. Gabriel	released 2005
Ed'Nimbus	Seeded filtration	Nucleotides	Local	server	P. Peterlongo et al.	2006
Geneious	Progressive/Iterative alignment; ClustalW plugin	Both	Local or Global	download	A.J. Drummond et al.	2005 / 2006
Kalign	Progressive alignment	Both	Global	serverEBI MPItoolkit	T. Lassmann	2005
MSA	Dynamic programming	Both	Local or Global	download	D.J. Lipman et al.	1989 (modified 1995)
PRRN/PRRP	Iterative alignment (especially refinement)	Protein	Local or Global	PRRP PRRN	Y. Totoki (based on O. Gotoh)	1991 and later
POA	Partial order/hidden Markov model	Protein	Local or Global	download	C. Lee	2002
SAM	Hidden Markov model	Protein	Local or Global	server	A. Krogh et al.	1994 (most recent version 2002)
MAFFT	Progressive/iterative alignment	Both	Local or Global	GenomeNet MAFFT	K. Katoh et al.	2005
MAVID	Progressive alignment	Both	Global	server	N. Bray and L. Pachter	2004
MULTALIN	Dynamic programming/clustering	Both	Local or Global	server	F. Corpet	1988
Multi-LAGAN	Progressive dynamic programming alignment	Both	Global	server	M. Brudno et al.	2003
MUSCLE	Progressive/iterative alignment	Both	Local or Global	server	R. Edgar	2004
ProbCons	Probabilistic/consistency	Protein	Local or Global	server	C. Do et al.	2005
PSAlign	Alignment preserving non-heuristic	Both	Local or Global	download	S.H. Sze, Y. Lu, Q. Yang.	2006
SAGA	Sequence alignment by genetic algorithm	Protein	Local or Global	download	C. Notredame et al.	1996 (new version 1998)
T-Coffee	More sensitive progressive alignment	Both	Local or Global	server	C. Notredame et al.	2000
RevTrans	Combines DNA and Protein alignment, by back translating the protein alignment to DNA.	DNA/Protein (special)	Local or Global	server	Wernersson and Pedersen	2003 (newest version 2005)
*Sequence Type: Protein or nucleotide. **Alignment Type: Local or global

Genomics analysis

Name	Description	Sequence Type*	Link
SLAM	Gene finding, alignment, annotation (human-mouse homology identification)	Nucleotide	server
Mauve	Multiple alignment of rearranged genomes	Nucleotide	download
MGA	Multiple Genome Aligner	Nucleotide	download
Mulan	Local multiple alignments of genome-length sequences	Nucleotide	server
Sequerome	Profiling sequence alignment data with major servers/services	Nucleotide/peptide	[1]
AVID	Pairwise global alignment with whole genomes	Nucleotide	server
SIBsim4 / Sim4	A program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns	Nucleotide	download
Shuffle-LAGAN	Pairwise glocal alignment of completed genome regions	Nucleotide	server
ACT (Artemis Comparison Tool)	Synteny and comparative genomics	Nucleotide	server
*Sequence Type: Protein or nucleotide

Motif finding

Name	Description	Sequence Type*	Link
MEME/MAST	Motif discovery and search	Both	server
BLOCKS	Ungapped motif identification from BLOCKS database	Both	server
eMOTIF	Extraction and identification of shorter motifs	Both	servers
Gibbs motif sampler	Stochastic motif extraction by statistical likelihood	Both	server (one of many implementations)
TEIRESIAS	Motif extraction and database search	Both	server
PRATT	Pattern generation for use with ScanProsite	Protein	server
ScanProsite	Motif database search tool	Protein	server
PHI-Blast	Motif search and alignment tool	Both	server
I-sites	Local structure motif library	Protein	server
*Sequence Type: Protein or nucleotide

Benchmarking

Name	Link	Authors
BAliBASE	download	Thompson, Plewniak, Poch
Prefab	download	Edgar

Viewers

Jalview is a Java multiple sequence alignment viewer, which is used to integrate the results of a secondary structure prediction via the JPred web server with a multiple sequence alignment given as input or derived during the run of the algorithm.

External links

• Pollard et al. (2004) (PubMed Central free fulltext): The authors discuss LAGAN, CHAOS, and Dialign as the most effective tools tested for certain uses.