List of sequence alignment software
Pairwise alignment
*Sequence type: protein or nucleotide **Alignment type: local or global

List of sequence alignment software

Section Title: Pairwise alignment
Table Section Text: *Sequence type: protein or nucleotide **Alignment type: local or global

Name	Description	Sequence type*	Alignment type**	Link	Author	Year

ACANA	Fast heuristic anchor based pairwise alignment	Both	Both	download	Huang, Umbach, Li	2005

AlignMe	Alignments for membrane protein sequences	Protein	Both	download, server	M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest	2013

ALLALIGN	For DNA, RNA and proteins with summed length n, generates all local alignments in O(n) time using approximate suffix tree matching or mapped density dynamic alignment	Both	Local	allalign	E. Wachtel	2017

Bioconductor Biostrings::pairwiseAlignment	Dynamic programming	Both	Both + Ends-free	site	P. Aboyoun	2008

BioPerl dpAlign	Dynamic programming	Both	Both + Ends-free	site	Y. M. Chan	2003

BLASTZ, LASTZ	Seeded pattern-matching	Nucleotide	Local	download, download	Schwartz et al.	2004,2009

CUDAlign	DNA sequence alignment of unrestricted size in single or multiple GPUs	Nucleotide	Local, SemiGlobal, Global	download	E. Sandes	2011-2015

DNADot	Web-based dot-plot tool	Nucleotide	Global	server	R. Bowen	1998

DNASTAR Lasergene Molecular Biology Suite	Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis.	Both	Both	DNASTAR site	DNASTAR	1993-2016

DOTLET	Java-based dot-plot tool	Both	Global	applet	M. Pagni and T. Junier	1998

FEAST	Posterior based local extension with descriptive evolution model	Nucleotide	Local	site	A. K. Hudek and D. G. Brown	2010

Genome Compiler Genome Compiler	Align chromatogram files (.ab1, .scf) against a template sequence, locate errors, and correct them instantly. Learn more	Nucleotide	Local	Free online & download	Genome Compiler Corporation	2014

G-PAS	GPU-based dynamic programming with backtracking	Both	Local, SemiGlobal, Global	site+download	W. Frohmberg, M. Kierzynka et al.	2011

GapMis	Does pairwise sequence alignment with one gap	Both	SemiGlobal	site	K. Frousios, T. Flouri, C. S. Iliopoulos, K. Park, S. P. Pissis, G. Tischler	2012

GGSEARCH, GLSEARCH	Global:Global (GG), Global:Local (GL) alignment with statistics	Protein	Global in query	FASTA server	W. Pearson	2007

JAligner	Java open-source implementation of Smith-Waterman	Both	Local	JWS	A. Moustafa	2005

K*Sync	Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores	Protein	Both	Robetta server	D. Chivian & D. Baker	2003

LALIGN	Multiple, non-overlapping, local similarity (same algorithm as SIM)	Both	Local non-overlapping	server FASTA server	W. Pearson	1991 (algorithm)

NW-align	Standard Needleman-Wunsch dynamic programming algorithm	Protein	Global	server and download	Y Zhang	2012

mAlign	modelling alignment; models the information content of the sequences	Nucleotide	Both	doc code[permanent dead link]	D. Powell, L. Allison and T. I. Dix	2004

matcher	Waterman-Eggert local alignment (based on LALIGN)	Both	Local	Pasteur	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	SemiGlobal	EMBL-EBIPasteur	A. Bleasby	1999

Ngila	logarithmic and affine gap costs and explicit models of indel evolution	Both	Global	download	R. Cartwright	2007

NW	Needleman-Wunsch dynamic programming	Both	Global	download	A.C.R. Martin	1990-2015

parasail	C/C++/Python/Java SIMD dynamic programming library for SSE, AVX2	Both	Global, Ends-free, Local	site	J. Daily	2015

Path	Smith-Waterman on protein back-translation graph (detects frameshifts at protein level)	Protein	Local	server download	M. Gîrdea et al.	2009

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

SABERTOOTH	Alignment using predicted Connectivity Profiles	Protein	Global	download on request[permanent dead link]	F. Teichert, J. Minning, U. Bastolla, and M. Porto	2009

Satsuma	Parallel whole-genome synteny alignments	DNA	Local	download	M.G. Grabherr et al.	2010

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

SPA: Super pairwise alignment	Fast pairwise global alignment	Nucleotide	Global	available upon request	Shen, Yang, Yao, Hwang	2002

SSEARCH	Local (Smith-Waterman) alignment with statistics	Protein	Local	EMBL-EBI FASTA server	W. Pearson	1981 (Algorithm)

Sequences Studio	Java applet demonstrating various algorithms from	Generic sequence	Local and global	code applet	A.Meskauskas	1997 (reference book)

SWIFT suit	Fast Local Alignment Searching	DNA	Local	site	K. Rasmussen, W. Gerlach	2005,2008

stretcher	Memory-optimized Needleman-Wunsch dynamic programming	Both	Global	Pasteur	I. Longden (modified from G. Myers and W. Miller)	1999

tranalign	Aligns nucleic acid sequences given a protein alignment	Nucleotide	NA	Pasteur	G. Williams (modified from B. Pearson)	2002

UGENE	Opensource Smith-Waterman for SSE/CUDA, Suffix array based repeats finder & dotplot	Both	Both	UGENE site	UniPro	2010

water	Smith-Waterman dynamic programming	Both	Local	EMBL-EBIPasteur	A. Bleasby	1999

wordmatch	k-tuple pairwise match	Both	NA	Pasteur	I. Longden	1998

YASS	Seeded pattern-matching	Nucleotide	Local	server download	L. Noe and G. Kucherov	2004

Sentence(s)

YASS is a pairwise sequence alignment software for nucleotide sequences.

final_sentence: YASS is a pairwise sequence alignment software for nucleotide sequences.