List of sequence alignment software

This list of sequence alignment software is a compilation of bioinformatics software tools and web portals used in pairwise sequence alignment, multiple sequence alignment, and structural alignment.

Pairwise alignment

NAME	Description	Sequence Type*	Alignment Type**	Link	Author	Year
DOTLET	Java-based dot-plot tool	Both	Global	applet	M. Pagni and T. Junier	1998
SIM	Local similarity	Both	Local	servers	X. Huang and W. Miller	1991
SIM, GAP, NAP, LAP	Local similarity with varying gap treatments	Both	Local and global	server	X. Huang	1990-6
LALIGN	Local similarity (same algorithm as SIM)	Both	Local (default) or global	server	B. Pearson	1991 (algorithm)
needle	Needleman-Wunsch dynamic programming	Both	Global	server	A. Bleasby	1999
water	Smith-Waterman dynamic programming	Both	Local	server	A. Bleasby	1999
tranalign	Aligns nucleic acid sequences given a protein alignment	Nucleotide	N/A	server	G. Williams (based on B. Pearson)	2002

*Sequence Type: Protein or nucleotide **Alignment Type: Local or global

Structural alignment

NAME	Description	Class	Type	Link	Author	Year
MAMMOTH	MAtching Molecular Models Obtained from Theory	Cα	Pair	server	AR. Ortiz	2002
CE/CE-MC	Combinatorial Extension -- Monte Carlo	Cα	Multi	server	I. Shindyalov	2000
DaliLite	Distance Matrix Alignment	C-Map	Pair	server	L. Holm	1993
VAST	Vector Alignment Search Tool	SSE	Pair	server	S. Bryant	1996
PrISM	Protein Informatics Systems for Modeling	SSE	Multi	server	B. Honig	2000
SSAP	Sequential Structure Alignment Program	SSE	Multi	server	C. Orengo	1989
SARF2	Spatial Arrangements of Backbone Fragments	SSE	Pair	server	D. Fischer	1996
KENOBI/K2	NA	SSE	Pair	server	Z. Weng	2000
STAMP	STructural Alignment of Multiple Proteins	Sequence	Multi	server	R. Russell and G. Barton	1992
MASS	Multiple Alignment by Secondary Structure	SSE	Multi	server	O. Dror and H. Wolfson	2003
MALECON	NA	Geometry	Multi	NA	S. Wodak	2004
MultiProt	Multiple Alignment of Protein Structures	Geometry	Multi	server	M. Shatsky and H. Wolfson	2004
SCALI	Structural Core ALIgnment of proteins	Sequence	Pair	server	C. Bystroff	2004
DEJAVU	NA	SSE	Pair	server	GJ. Kleywegt	1997
SSM	Secondary Structure Matching	SSE/Cα	Multi	server	E. Krissinel	2003
SHEBA	Structural Homology by Environment-Based Alignment	Sequence	Pair	server	B. Lee	2000
LGA	Local-Global Alignment	Sequence	Pair	server	A. Zemla	2003
POSA	Partial Order Structure Alignment	Cα	Multi	server	Y. Ye and A. Godzik	2005
FATCAT	Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists	Cα	Pair	server	Y. Ye and A. Godzik	2004
Matras	MArkovian TRAnsition of protein Structure	Cα & SSE	Pair	NA	K. Nishikawa	2000
MAMMOTH-mult	MAMMOTH-based multiple structure alignment	Cα	Multi	server	D. Lupyan	2005
Protein3Dfit	NA	C-Map	Pair	server	D. Schomburg	1994
PRIDE	PRobaility of IDEntity	Cα	Pair	server	S. Pongor	2002
FAST	FAST Alignment and Search Tool	Cα	Pair	server	J. Zhu	2004
C-BOP	Coordinate-Based Organization of Proteins	N/A	Multi	server	E. Sandelin	2005
ProFit	Protein least-squares Fitting	Cα	Multi	server	ACR. Martin	1996
TOPOFIT	Alignment as a superimposition of common volumes at a topomax point	Cα	Pair	server	V. A. Ilyin	2004
MUSTANG	MUltiple STructural AligNment AlGorithm	Cα & C-Map	Multi	download	A.S. Konagurthu et al.	2005
URMS	Unit-vector RMSD	Cα	Pair	server	K. Kedem	2003
LOCK	Hierarchical protein structure superposition	SSE	Pair	NA	AP. Singh	1997
LOCK 2	Improvements over LOCK	SSE	Pair	NA	J. Shapiro	2003
CBA	Consistency Based Alignment	SSE	Multi	server	J. Ebert	2006
TetraDA	Tetrahedral Decomposition Alignment	SSE	Multi	NA	J. Roach	2005
STRAP	STRucture based Alignment Program	Cα	Multi	server	C. Gille	2006

Key map:

• Cα -- Backbone Atom (Cα) Alignment;
• SSE -- Secondary Structure Elements Alignment;
• Pair -- Pairwise Alignment (2 structures *only*);
• Multi -- Multiple Structure Alignment (MStA);
• C-Map -- Contact Map