Pairwise alignment

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NameDescriptionSequence Type*Alignment Type**LinkAuthorYear
ACANAfast heuristic anchor based pairwise alignmentBothBothdownloadHuang, Umbach, Li2005
AlignMeAlignments for membrane protein sequencesProteinBothdownload,serverM. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest2013
BioconductorBiostrings::pairwiseAlignmentDynamic programmingBothBoth + Ends-freesiteP. Aboyoun2008
BioPerl dpAlignDynamic programmingBothBoth + Ends-freesiteY. M. Chan2003
BLASTZ,LASTZSeeded pattern-matchingNucleotideLocaldownload,downloadSchwartz et al.[9][10]2004,2009
DNADotWeb-based dot-plot toolNucleotideGlobalserverR. Bowen1998
DOTLETJava-based dot-plot toolBothGlobalappletM. Pagni and T. Junier1998
FEASTPosterior based local extension with descriptive evolution modelNucleotideLocalsiteA. K. Hudek and D. G. Brown2010
G-PASGPU-based dynamic programming with backtrackingBothLocal, SemiGlobal, Globalsite+downloadW. Frohmberg, M. Kierzynka et al.2011
GapMisGapMis is a tool for pairwise sequence alignment with a single gapBothSemiGlobalsiteK. Frousios, T. Flouri, C. S. Iliopoulos, K. Park, S. P. Pissis, G. Tischler2012
GGSEARCH, GLSEARCHGlobal:Global (GG), Global:Local (GL) alignment with statisticsProteinGlobal in queryFASTA serverW. Pearson2007
JAlignerOpen source Java implementation of Smith-WatermanBothLocalJWSA. Moustafa2005
K*SyncProtein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scoresProteinBothRobetta serverD. Chivian & D. Baker [11]2003
LALIGNMultiple, non-overlapping, local similarity (same algorithm as SIM)BothLocal non-overlappingserver FASTA serverW. Pearson1991 (algorithm)
NW-alignStandard Needleman-Wunsch dynamic programming algorithmProteinGlobalserver and downloadY Zhang2012
mAlignmodelling alignment; models the information content of the sequencesNucleotideBothdoc codeD. Powell, L. Allison and T. I. Dix2004
matcherWaterman-Eggert local alignment (based on LALIGN)BothLocalPasteurI. Longden (modified from W. Pearson)1999
MCALIGN2explicit models of indel evolutionDNAGlobalserverJ. Wang et al.2006
MUMmersuffix tree basedNucleotideGlobaldownloadS. Kurtz et al.2004
needleNeedleman-Wunsch dynamic programmingBothSemiGlobalEMBL-EBIPasteurA. Bleasby1999
Ngilalogarithmic and affine gap costs and explicit models of indel evolutionBothGlobaldownloadR. Cartwright2007
PathSmith-Waterman on protein back-translationgraph (detects frameshifts at protein level)ProteinLocalserver downloadM. Gîrdea et al.[12]2009
PatternHunterSeeded pattern-matchingNucleotideLocaldownloadB. Ma et al.[13][14]2002–2004
ProbA (also propA)Stochastic partition function sampling viadynamic programmingBothGlobaldownloadU. Mückstein2002
PyMOL"align" command aligns sequence & applies it to structureProteinGlobal (by selection)siteW. L. DeLano2007
REPutersuffix tree basedNucleotideLocaldownloadS. Kurtz et al.2001
SABERTOOTHAlignment using predicted Connectivity ProfilesProteinGlobaldownload on requestF. Teichert, J. Minning, U. Bastolla, and M. Porto2009
SatsumaParallel whole-genome synteny alignmentsDNALocaldownloadM.G. Grabherret al.2010
SEQALNVarious dynamic programmingBothLocal or GlobalserverM.S. Waterman and P. Hardy1996
SIM, GAP, NAP, LAPLocal similarity with varying gap treatmentsBothLocal or globalserverX. Huang and W. Miller1990-6
SIMLocal similarityBothLocalserversX. Huang and W. Miller1991
SPA: Super pairwise alignmentFast pairwise global alignmentNucleotideGlobalavailable upon requestShen, Yang, Yao, Hwang2002
SSEARCHLocal (Smith-Waterman) alignment with statisticsProteinLocalEMBL-EBI FASTA serverW. Pearson1981 (Algorithm)
Sequences StudioJava applet demonstrating various algorithms from [15]Generic sequenceLocal and globalcode appletA.Meskauskas1997 (reference book)
SWIFT suitFast Local Alignment SearchingDNALocalsiteK. Rasmussen,[16]W. Gerlach2005,2008
stretcherMemory-optimized Needleman-Wunsch dynamic programmingBothGlobalPasteurI. Longden (modified from G. Myers and W. Miller)1999
tranalignAligns nucleic acid sequences given a protein alignmentNucleotideNAPasteurG. Williams (modified from B. Pearson)2002
UGENEOpensource Smith-Waterman for SSE/CUDA, Suffix array based repeats finder & dotplotBothBothUGENE siteUniPro2010
waterSmith-Waterman dynamic programmingBothLocalEMBL-EBIPasteurA. Bleasby1999
wordmatchk-tuple pairwise matchBothNAPasteurI. Longden1998
YASSSeeded pattern-matchingNucleotideLocalserver downloadL. Noe and G. Kucherov [17]2004–2011

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Multiple sequence alignment

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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. Morge
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