List of sequence alignment software

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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.

Name Description Sequence type* Alignment type** Author Year License ABA A Bruijn alignment Protein Global B. Raphael et al. 2004 , freeware for education, research, nonprofit ALE manual alignment ; some software assistance Nucleotides Local J. Blandy and K. Fogel 1994 (latest version 2007) , GPL2ALLALIGNFor DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater, MSA or within a single molecule. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. BothLocalE. Wachtel2017Free AMAP Sequence annealing Both Global A. Schwartz and L. Pachter 2006 anon. fast, optimal alignment of three sequences using linear gap costs Nucleotides Global D. Powell, L. Allison and T. I. Dix 2000 BAli Phy Tree+multi alignment; probabilistic Bayesian; joint estimation Both + Codons Global BD Redelings and MA Suchard 2005 (latest version 2018) , GPL Base By Base Java based multiple sequence alignment editor with integrated analysis tools Both Local or global R. Brodie et al. 2004 , freeware, must register CHAOS, DIALIGN Iterative alignment Both Local (preferred) M. Brudno and B. Morgenstern 2003 ClustalW Progressive alignment Both Local or global Thompson et al. 1994 , LGPL CodonCode Aligner Multi alignment; ClustalW & Phrap support Nucleotides Local or global P. Richterich et al. 2003 (latest version 2009) Compass COmparison of Multiple Protein sequence Alignments with assessment of Statistical Significance Protein Global R. I. Sadreyev, et al. 2009 DECIPHER Progressive iterative alignment Both Global Erik S. Wright 2014 , GPL DIALIGN TX and DIALIGN T Segment based method Both Local (preferred) or Global A. R. Subramanian 2005 (latest version 2008) DNA Alignment Segment based method for intraspecific alignments Both Local (preferred) or Global A. Roehl 2005 (latest version 2008) DNA Baser Sequence Assembler Multi alignment; Full automatic sequence alignment; Automatic ambiguity correction; Internal base caller; Command line seq alignment Nucleotides Local or global Heracle BioSoft SRL 2006 (latest version 2018) Commercial (some modules are freeware) DNADynamo linked DNA to Protein multiple alignment with MUSCLE, Clustal and Smith Waterman Both Local or global DNADynamo 2004 (newest version 2017) EDNA Energy Based Multiple Sequence Alignment for DNA Binding Sites Nucleotides Local or global Salama, RA. et al. 2013 FAMSAProgressive alignment for extremely large protein families (hundreds of thousands of members)ProteinGlobalDeorowicz et al.2016, GPL 3 FSA Sequence annealing Both Global R. K. Bradley et al. 2008 Geneious Progressive Iterative alignment; ClustalW plugin Both Local or global A. J. Drummond et al. 2005 (latest version 2017) GUIDANCE Quality control and filtering of multiple sequence alignments Both Local or global O. Penn et al. 2010 (latest version 2015) Kalign Progressive alignment Both Global T. Lassmann 2005 MACSEProgressive iterative alignment. Multiple alignment of coding sequences accounting for frameshifts and stop codons. NucleotidesGlobalV. Ranwez et al.2011 (latest version, v2.07 2023) MAFFT Progressive iterative alignment Both Local or global K. Katoh et al. 2005 , BSD MARNA Multi alignment of RNAs RNA Local S. Siebert et al. 2005 MAVID Progressive alignment Both Global N. Bray and L. Pachter 2004 MegAlign Pro (Lasergene Molecular Biology) 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 Local or global DNASTAR 1993 2023 MSA Dynamic programming Both Local or global D. J. Lipman et al. 1989 (modified 1995) MSAProbs Dynamic programming Protein Global Y. Liu, B. Schmidt, D. Maskell 2010 MULTALIN Dynamic programming clustering Both Local or global F. Corpet 1988 Multi LAGAN Progressive dynamic programming alignment Both Global M. Brudno et al. 2003 MUSCLE Progressive iterative alignment Both Local or global R. Edgar 2004 Opal Progressive iterative alignment Both Local or global T. Wheeler and J. Kececioglu 2007 (latest stable 2013, latest beta 2016) Pecan Probabilistic consistency DNA Global B. Paten et al. 2008 Phylo A human computing framework for comparative genomics to solve multiple alignment Nucleotides Local or global McGill Bioinformatics 2010 PMFastR Progressive structure aware alignment RNA Global D. DeBlasio, J Braund, S Zhang 2009 Praline Progressive iterative consistency homology extended alignment with preprofiling and secondary structure prediction Protein Global J. Heringa 1999 (latest version 2009) PicXAA Nonprogressive, maximum expected accuracy alignment Both Global S. M. E. Sahraeian and B. J. Yoon 2010 POA Partial order/hidden Markov model Protein Local or global C. Lee 2002 Probalign Probabilistic/consistency with partition function probabilities Protein Global Roshan and Livesay 2006 , public domain ProbCons Probabilistic/consistency Protein Local or global C. Do et al. 2005 , public domain PROMALS3D Progressive alignment/hidden Markov model/Secondary structure/3D structure Protein Global J. Pei et al. 2008 PRRN/PRRP Iterative alignment (especially refinement) Protein Local or global Y. Totoki (based on O. Gotoh) 1991 and later PSAlign Alignment preserving non heuristic Both Local or global 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 Wernersson and Pedersen 2003 (newest version 2005) SAGA Sequence alignment by genetic algorithm Protein Local or global C. Notredame et al. 1996 (new version 1998) SAM Hidden Markov model Protein Local or global A. Krogh et al. 1994 (most recent version 2002) Se Al Manual alignment Both Local A. Rambaut 2002 StatAlign Bayesian co estimation of alignment and phylogeny (MCMC) Both Global A. Novak et al. 2008 Stemloc Multiple alignment and secondary structure prediction RNA Local or global I. Holmes 2005 , GPL 3 (parte de DART) T Coffee More sensitive progressive alignment Both Local or global C. Notredame et al. 2000 (newest version 2008) , GPL 2 UGENE Supports multiple alignment with MUSCLE, KAlign, Clustal and MAFFT plugins Both Local or global UGENE team 2010 (newest version 2020) , GPL 2 VectorFriends VectorFriends Aligner, MUSCLE plugin, and ClustalW plugin Both Local or global BioFriends team 2013 , freeware for academic use GLProbs Adaptive pair Hidden Markov Model based approach Protein Global Y. Ye et al. 2013
*Sequence type: protein or nucleotide. **Alignment type: local or global

Name Authors PFAM 30.0 (2016) SMART (2015) Letunic, Copley, Schmidt, Ciccarelli, Doerks, Schultz, Ponting, Bork BAliBASE 3 (2015) Thompson, Plewniak, Poch Oxbench (2011) Raghava, Searle, Audley, Barber, Barton Benchmark collection (2009) Edgar HOMSTRAD (2005) Mizuguchi PREFAB 4.0 (2005) Edgar SABmark (2004) Van Walle, Lasters, Wyns

Please see List of alignment visualization software.

Name Description paired end option Use FASTQ quality Gapped Multi threaded License Reference Year Arioc Computes Smith Waterman gapped alignments and mapping qualities on one or more GPUs. Supports BS seq alignments. Processes 100,000 to 500,000 reads per second (varies with data, hardware, and configured sensitivity). , BSD 2015 BarraCUDA A GPGPU accelerated Burrows–Wheeler transform (FM index) short read alignment program based on BWA, supports alignment of indels with gap openings and extensions. , POSIX Threads and CUDA , GPL BBMap Uses a short kmers to rapidly index genome; no size or scaffold count limit. Higher sensitivity and specificity than Burrows–Wheeler aligners, with similar or greater speed. Performs affine transform optimized global alignment, which is slower but more accurate than Smith Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data. Splice aware; capable of processing long indels and RNA seq. Pure Java; runs on any platform. Used by the Joint Genome Institute. , BSD 2010 BFAST Explicit time and accuracy tradeoff with a prior accuracy estimation, supported by indexing the reference sequences. Optimally compresses indexes. Can handle billions of short reads. Can handle insertions, deletions, SNPs, and color errors (can map ABI SOLiD color space reads). Performs a full Smith Waterman alignment. , POSIX Threads , GPL 2009 BigBWA Runs the Burrows–Wheeler Aligner BWA on a Hadoop cluster. It supports the algorithms BWA MEM, BWA ALN, and BWA SW, working with paired and single reads. It implies an important reduction in the computational time when running in a Hadoop cluster, adding scalability and fault tolerance. Low quality bases trimming , GPL 3 2015 BLASTN BLAST's nucleotide alignment program, slow and not accurate for short reads, and uses a sequence database (EST, Sanger sequence) rather than a reference genome. BLAT Made by Jim Kent. Can handle one mismatch in initial alignment step. , client server , freeware for academic and noncommercial use2002 Bowtie Uses a Burrows–Wheeler transform to create a permanent, reusable index of the genome; 1.3 GB memory footprint for human genome. Aligns more than 25 million Illumina reads in 1 CPU hour. Supports Maq like and SOAP like alignment policies , POSIX Threads , Artistic2009 BWA Uses a Burrows–Wheeler transform to create an index of the genome. It's a bit slower than Bowtie but allows indels in alignment. Low quality bases trimming , GPL 2009 BWA PSSM A probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). The aligner is adaptable in the sense that it can take into account the quality scores of the reads and models of data specific biases, such as those observed in Ancient DNA, PAR CLIP data or genomes with biased nucleotide compositions. 2014 CASHX Quantify and manage large quantities of short read sequence data. CASHX pipeline contains a set of tools that can be used together, or separately as modules. This algorithm is very accurate for perfect hits to a reference genome. , freeware for academic and noncommercial use Cloudburst Short read mapping using Hadoop MapReduce , Hadoop MapReduce , Artistic CUDA EC Short read alignment error correction using GPUs. , GPU enabledCUSHAW A CUDA compatible short read aligner to large genomes based on Burrows–Wheeler transform (GPU enabled) , GPL2012CUSHAW2 Gapped short read and long read alignment based on maximal exact match seeds. This aligner supports both base space (e. g. from Illumina, 454, Ion Torrent and PacBio sequencers) and ABI SOLiD color space read alignments. , GPL 2014CUSHAW2 GPU GPU accelerated CUSHAW2 short read aligner. , GPL CUSHAW3 Sensitive and accurate base space and color space short read alignment with hybrid seeding , GPL 2012 drFAST Read mapping alignment software that implements cache obliviousness to minimize main/cache memory transfers like mrFAST and mrsFAST, however designed for the SOLiD sequencing platform (color space reads). It also returns all possible map locations for improved structural variation discovery. , for structural variation , BSD ELAND Implemented by Illumina. Includes ungapped alignment with a finite read length. ERNE Extended Randomized Numerical alignEr for accurate alignment of NGS reads. It can map bisulfite treated reads. Low quality bases trimming Multithreading and MPI enabled , GPL 3GASSST Finds global alignments of short DNA sequences against large DNA banks Multithreading CeCILL version 2 License. 2011 GEM High quality alignment engine (exhaustive mapping with substitutions and indels). More accurate and several times faster than BWA or Bowtie 1/2. Many standalone biological applications (mapper, split mapper, mappability, and other) provided. , GPL32012Genalice MAP Ultra fast and comprehensive NGS read aligner with high precision and small storage footprint. Low quality bases trimming , commercialGeneious Assembler Fast, accurate overlap assembler with the ability to handle any combination of sequencing technology, read length, any pairing orientations, with any spacer size for the pairing, with or without a reference genome. , commercial GensearchNGS Complete framework with user friendly GUI to analyse NGS data. It integrates a proprietary high quality alignment algorithm and plug in ability to integrate various public aligner into a framework allowing to import short reads, align them, detect variants, and generate reports. It is made for resequencing projects, namely in a diagnostic setting. , commercialGMAP and GSNAP Robust, fast short read alignment. GMAP: longer reads, with multiple indels and splices (see entry above under Genomics analysis); GSNAP: shorter reads, with one indel or up to two splices per read. Useful for digital gene expression, SNP and indel genotyping. Developed by Thomas Wu at Genentech. Used by the National Center for Genome Resources (NCGR) in Alpheus. , freeware for academic and noncommercial useGNUMAP Accurately performs gapped alignment of sequence data obtained from next generation sequencing machines (specifically of Solexa Illumina) back to a genome of any size. Includes adaptor trimming, SNP calling and Bisulfite sequence analysis. , also supports Illumina * int. txt and * prb. txt files with all 4 quality scores for each base Multithreading and MPI enabled 2009 HIVE hexagon Uses a hash table and bloom matrix to create and filter potential positions on the genome. For higher efficiency uses cross similarity between short reads and avoids realigning non unique redundant sequences. It is faster than Bowtie and BWA and allows indels and divergent sensitive alignments on viruses, bacteria, and more conservative eukaryotic alignments. , freeware for academic and noncommercial users registered to HIVE deployment instance 2014 IMOS Improved Meta aligner and Minimap2 On Spark. A long read distributed aligner on Apache Spark platform with linear scalability w. r. t. single node execution. Isaac Fully uses all the computing power available on one server node; thus, it scales well over a broad range of hardware architectures, and alignment performance improves with hardware abilities , GPL LAST Uses adaptative seeds and copes more efficiently with repeat rich sequences (e. g. genomes). For example: it can align reads to genomes without repeat masking, without becoming overwhelmed by repetitive hits. , GPL 2011 MAQ Ungapped alignment that takes into account quality scores for each base. , GPL mrFAST, mrsFAST Gapped (mrFAST) and ungapped (mrsFAST) alignment software that implements cache obliviousness to minimize main/cache memory transfers. They are designed for the Illumina sequencing platform and they can return all possible map locations for improved structural variation discovery. , for structural variation , BSD MOM MOM or maximum oligonucleotide mapping is a query matching tool that captures a maximal length match within the short read. MOSAIK Fast gapped aligner and reference guided assembler. Aligns reads using a banded Smith Waterman algorithm seeded by results from a k mer hashing scheme. Supports reads ranging in size from very short to very long. MPscan Fast aligner based on a filtration strategy (no indexing, use q grams and Backward Nondeterministic DAWG Matching) 2009 Novoalign & NovoalignCS Gapped alignment of single end and paired end Illumina GA I & II, ABI Colour space & ION Torrent reads. High sensitivity and specificity, using base qualities at all steps in the alignment. Includes adapter trimming, base quality calibration, Bi Seq alignment, and options for reporting multiple alignments per read. Use of ambiguous IUPAC codes in reference for common SNPs can improve SNP recall and remove allelic bias. Multi threading and MPI versions available with paid license , freeware single threaded version for academic and noncommercial use NextGENe Developed for use by biologists performing analysis of next generation sequencing data from Roche Genome Sequencer FLX, Illumina GA/HiSeq, Life Technologies Applied BioSystems’ SOLiD System, PacBio and Ion Torrent platforms. , commercial NextGenMap Flexible and fast read mapping program (twice as fast as BWA), achieves a mapping sensitivity comparable to Stampy. Internally uses a memory efficient index structure (hash table) to store positions of all 13 mers present in the reference genome. Mapping regions where pairwise alignments are required are dynamically determined for each read. Uses fast SIMD instructions (SSE) to accelerate alignment calculations on CPU. If available, alignments are computed on GPU (using OpenCL/CUDA) further reducing runtime 20 50%. , POSIX Threads, OpenCL/CUDA, SSE 2013 Omixon Variant Toolkit Includes highly sensitive and highly accurate tools for detecting SNPs and indels. It offers a solution to map NGS short reads with a moderate distance (up to 30% sequence divergence) from reference genomes. It poses no restrictions on the size of the reference, which, combined with its high sensitivity, makes the Variant Toolkit well suited for targeted sequencing projects and diagnostics. , commercial PALMapper Efficiently computes both spliced and unspliced alignments at high accuracy. Relying on a machine learning strategy combined with a fast mapping based on a banded Smith Waterman like algorithm, it aligns around 7 million reads per hour on one CPU. It refines the originally proposed QPALMA approach. , GPL Partek Flow For use by biologists and bioinformaticians. It supports ungapped, gapped and splice junction alignment from single and paired end reads from Illumina, Life technologies Solid TM, Roche 454 and Ion Torrent raw data (with or without quality information). It integrates powerful quality control on FASTQ/Qual level and on aligned data. Additional functionality include trimming and filtering of raw reads, SNP and InDel detection, mRNA and microRNA quantification and fusion gene detection. Multiprocessor core, client server installation possible , commercial, free trial version PASS Indexes the genome, then extends seeds using pre computed alignments of words. Works with base space, color space (SOLID), and can align genomic and spliced RNA seq reads. , freeware for academic and noncommercial use PerM Indexes the genome with periodic seeds to quickly find alignments with full sensitivity up to four mismatches. It can map Illumina and SOLiD reads. Unlike most mapping programs, speed increases for longer read lengths. , GPL PRIMEX Indexes the genome with a k mer lookup table with full sensitivity up to an adjustable number of mismatches. It is best for mapping 15 60 bp sequences to a genome. , multiple processes per search 2003 QPalma Can use quality scores, intron lengths, and computation splice site predictions to perform and performs an unbiased alignment. Can be trained to the specifics of a RNA seq experiment and genome. Useful for splice site/intron discovery and for gene model building. (See PALMapper for a faster version). , client server , GPL 2 RazerS No read length limit. Hamming or edit distance mapping with configurable error rates. Configurable and predictable sensitivity (runtime/sensitivity tradeoff). Supports paired end read mapping. , LGPL REAL, cREAL REAL is an efficient, accurate, and sensitive tool for aligning short reads obtained from next generation sequencing. The programme can handle an enormous amount of single end reads generated by the next generation Illumina/Solexa Genome Analyzer. cREAL is a simple extension of REAL for aligning short reads obtained from next generation sequencing to a genome with circular structure. , GPL RMAP Can map reads with or without error probability information (quality scores) and supports paired end reads or bisulfite treated read mapping. There are no limitations on read length or number of mismatches. , GPL 3rNA A randomized Numerical Aligner for Accurate alignment of NGS reads Low quality bases trimming Multithreading and MPI enabled , GPL 3 RTG Investigator Extremely fast, tolerant to high indel and substitution counts. Includes full read alignment. Product includes comprehensive pipelines for variant detection and metagenomic analysis with any combination of Illumina, Complete Genomics and Roche 454 data. , for variant calling , freeware for individual investigator use Segemehl Can handle insertions, deletions, mismatches; uses enhanced suffix arrays , freeware for noncommercial use2009 SeqMap Up to 5 mixed substitutions and insertions deletions; various tuning options and input output formats , freeware for academic and noncommercial use Shrec Short read error correction with a suffix tree data structure , Java SHRiMP Indexes the reference genome as of version 2. Uses masks to generate possible keys. Can map ABI SOLiD color space reads. , OpenMP , [[BSD licenses , BSD]] derivative 2009 2011 SLIDER Slider is an application for the Illumina Sequence Analyzer output that uses the "probability" files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. 2009 2010 SOAP, SOAP2, SOAP3, SOAP3 dp SOAP: robust with a small (1 3) number of gaps and mismatches. Speed improvement over BLAT, uses a 12 letter hash table. SOAP2: using bidirectional BWT to build the index of reference, and it is much faster than the first version. SOAP3: GPU accelerated version that could find all 4 mismatch alignments in tens of seconds per one million reads. SOAP3 dp, also GPU accelerated, supports arbitrary number of mismatches and gaps according to affine gap penalty scores. , SOAP3 dp , POSIX Threads; SOAP3, SOAP3 dp need GPU with CUDA support , GPL SOCS For ABI SOLiD technologies. Significant increase in time to map reads with mismatches (or color errors). Uses an iterative version of the Rabin Karp string search algorithm. , GPLSparkBWA Integrates the Burrows–Wheeler Aligner (BWA) on an Apache Spark framework running atop Hadoop. Version 0.2 of October 2016, supports the algorithms BWA MEM, BWA backtrack, and BWA ALN. All of them work with single reads and paired end reads. Low quality bases trimming , GPL 32016 SSAHA, SSAHA2 Fast for a small number of variants , freeware for academic and noncommercial use Stampy For Illumina reads. High specificity, and sensitive for reads with indels, structural variants, or many SNPs. Slow, but speed increased dramatically by using BWA for first alignment pass. , freeware for academic and noncommercial use 2010 SToRM For Illumina or ABI SOLiD reads, with SAM native output. Highly sensitive for reads with many errors, indels (full from 0 to 15, extended support otherwise). Uses spaced seeds (single hit) and a very fast SSE SSE2 AVX2 AVX 512 banded alignment filter. For fixed length reads only, authors recommend SHRiMP2 otherwise. , OpenMP 2010 Subread, Subjunc Superfast and accurate read aligners. Subread can be used to map both gDNA seq and RNA seq reads. Subjunc detects exon exon junctions and maps RNA seq reads. They employ a novel mapping paradigm named seed and vote. , GPL 3 Taipan De novo assembler for Illumina reads , freeware for academic and noncommercial use UGENE Visual interface both for Bowtie and BWA, and an embedded aligner , GPL VelociMapper FPGA accelerated reference sequence alignment mapping tool from TimeLogic. Faster than Burrows–Wheeler transform based algorithms like BWA and Bowtie. Supports up to 7 mismatches and/or indels with no performance penalty. Produces sensitive Smith–Waterman gapped alignments. , commercial XpressAlign FPGA based sliding window short read aligner which exploits the embarrassingly parallel property of short read alignment. Performance scales linearly with number of transistors on a chip (i. e. performance guaranteed to double with each iteration of Moore's Law without modification to algorithm). Low power consumption is useful for datacentre equipment. Predictable runtime. Better price/performance than software sliding window aligners on current hardware, but not better than software BWT based aligners currently. Can manage large numbers (>2) of mismatches. Will find all hit positions for all seeds. Single FPGA experimental version, needs work to develop it into a multi FPGA production version. , freeware for academic and noncommercial use ZOOM 100% sensitivity for a reads between 15 and 240 bp with practical mismatches. Very fast. Support insertions and deletions. Works with Illumina & SOLiD instruments, not 454. Yes (GUI), no (CLI) , commercial