Multiple sequence alignment

Name	Description	Sequence Type*	Alignment Type**	Link	Author	Year	License
ABA	A-Bruijn alignment	Protein	Global	download	B.Raphael et al.	2004	Proprietary, without charge for educational, research and non profit.
ALE	manual alignment ; some software assistance	Nucleotides	Local	download	J. Blandy and K. Fogel	1994 (latest version 2007)	GPL2
AMAP	Sequence annealing	Both	Global	server	A. Schwartz and L. Pachter	2006
anon.	fast, optimal alignment of three sequences using linear gap costs	Nucleotides	Global	paper software	D. Powell, L. Allison and T. I. Dix	2000
BAli-Phy	Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation	Both	Global	WWW+download	BD Redelings and MA Suchard	2005 (latest version 2015)	GPL
Base-By-Base	Java-based multiple sequence alignment editor with integrated analysis tools	Both	Local or Global	download	R. Brodie et al.	2004	Free, requires registration.
CHAOS/DIALIGN	Iterative alignment	Both	Local (preferred)	server	M. Brudno and B. Morgenstern	2003
ClustalW	Progressive alignment	Both	Local or Global	download EMBL-EBIDDBJ PBIL EMBNetGenomeNet	Thompson et al.	1994	GNU Lesser GPL
CodonCode Aligner	Multi alignment; ClustalW & Phrap support	Nucleotides	Local or Global	download	P. Richterich et al.	2003 (latest version 2009)
Compass	COmparison of Multiple Protein sequence Alignments with assessment of Statistical Significance	Protein	Global	download and server	R.I. Sadreyev, et al.	2009
DECIPHER	Progressive/iterative alignment	Both	Global	download	Erik S. Wright	2014	GPL
DIALIGN-TX and DIALIGN-T	Segment-based method	Both	Local (preferred) or Global	download and server	A.R.Subramanian	2005 (latest version 2008)
DNA Alignment	Segment-based method for intraspecific alignments	Both	Local (preferred) or Global	server	A.Roehl	2005 (latest version 2008)
DNA Baser Sequence Assembler	Multi alignment; Automatic batch alignment	Nucleotides	Local or Global	www.DnaBaser.com	Heracle BioSoft	2006 (latest version 2014)
EDNA	Energy Based Multiple Sequence Alignment for DNA Binding Sites	Nucleotides	Local or Global	sourceforge.net/projects/msa-edna/	Salama, RA. et al.	2013
FSA	Sequence annealing	Both	Global	download and server	R. K. Bradley et al.	2008
Geneious	Progressive/Iterative alignment; ClustalW plugin	Both	Local or Global	download	A.J. Drummondet al.	2005 (latest version 2009)
Kalign	Progressive alignment	Both	Global	serverEMBL-EBIMPItoolkit	T. Lassmann	2005
MAFFT	Progressive/iterative alignment	Both	Local or Global	GenomeNet MAFFT	K. Katoh et al.	2005
MARNA	Multiple Alignment of RNAs	RNA	Local	server download	S. Siebert et al.	2005
MAVID	Progressive alignment	Both	Global	server	N. Bray and L. Pachter	2004
MSA	Dynamic programming	Both	Local or Global	download	D.J. Lipman et al.	1989 (modified 1995)
MSAProbs	Dynamic programming	Protein	Global	download	Y. Liu, B. Schmidt, D. Maskell	2010
MULTALIN	Dynamic programming/clustering	Both	Local or Global	server download	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
Opal	Progressive/iterative alignment	Both	Local or Global	download	T. Wheeler and J. Kececioglu	2007
Pecan	Probabilistic/consistency	DNA	Global	download	B. Paten et al.	2008
Phylo	A human computing framework for comparative genomics to solve multiple alignment	Nucleotides	Local or Global	site	McGill Bioinformatics	2010
Praline	Progressive/iterative/consistency/homology-extended alignment with pre-profiling and secondary structure prediction	Protein	Global	server	J. Heringa	1999 (latest version 2009)
PicXAA	non-progressive/maximum expected accuracy alignment	Both	Global	download and server	S.M.E. Sahraeian and B.J. Yoon	2010
POA	Partial order/hidden Markov model	Protein	Local or Global	download	C. Lee	2002
Probalign	Probabilistic/consistency with partition function probabilities	Protein	Global	server	Roshan and Livesay	2006
ProbCons	Probabilistic/consistency	Protein	Local or Global	server	C. Do et al.	2005
PROMALS3D	Progressive alignment/hidden Markov model/Secondary structure/3D structure	Protein	Global	server	J. Pei et al.	2008
PRRN/PRRP	Iterative alignment (especially refinement)	Protein	Local or Global	PRRP PRRN	Y. Totoki (based on O. Gotoh)	1991 and later
PSAlign	Alignment preserving non-heuristic	Both	Local or Global	download	S.H. Sze, Y. Lu, Q. Yang.	2006
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)
SAGA	Sequence alignment by genetic algorithm	Protein	Local or Global	download	C. Notredame et al.	1996 (new version 1998)
SAM	Hidden Markov model	Protein	Local or Global	server	A. Krogh et al.	1994 (most recent version 2002)
Se-Al	Manual alignment	Both	Local	download	A. Rambaut	2002
StatAlign	Bayesian co-estimation of alignment and phylogeny (MCMC)	Both	Global	download	A. Novak et al.	2008
Stemloc	Multiple alignment and secondary structure prediction	RNA	Local or Global	download	I. Holmes	2005	GPLv3 (parte deDART)
T-Coffee	More sensitive progressive alignment	Both	Local or Global	server download	C. Notredame et al.	2000 (newest version 2008)	GPL2
UGENE	Supports multiple alignment with MUSCLE, KAlign, Clustal and MAFFT plugins	Both	Local or Global	download	UGENE team	2010 (newest version 2012)	GPL2
VectorFriends	VectorFriends Aligner, MUSCLE plugin, andClustalW plugin	Both	Local or Global	download	BioFriends team	2013	Proprietary, but free for academic researchers
GLProbs	Adaptive pair-Hidden Markov Model based approach	Protein	Global	download	Y. Ye et al.	2013