6014:
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.
5305:
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).
5077:
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
6013:
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
3981:
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
5151:
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.
4748:
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,
4679:
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.
4190:
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
5360:
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
5179:
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
5008:
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
4645:
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
5649:
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
5117:
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
4434:
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.
3943:
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
4898:
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.
5451:
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.
2521:
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
1204:
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
4548:
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.
4718:
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.
4021:
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.
117:
NCBI compliant multinode and multicore BLAST wrapper. Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each
4222:
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.
5043:
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.
4341:
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.
5248:
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.
5078:
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%.
3870:
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).
1915:
For 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.
4614:
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.
5621:
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.
4840:
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.
5389:
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.
4120:
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
5875:
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
5334:
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.
5180:
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.
4810:
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
5789:
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.
804:
For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter.
6044:
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.
5111:
5688:
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.
5650:
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.
5214:
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.
6392:
Remmert, Michael; Biegert, Andreas; Hauser, Andreas; Söding, Johannes (2011-12-25). "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment".
550:
Retrieve and Relate (R&R) is a high performance yet sensitive multi-database search engine, capable of searching in parallel through DNA,RNA and Protein sequences.
8373:
Searls, David B.; Hoffmann, Steve; Otto, Christian; Kurtz, Stefan; Sharma, Cynthia M.; Khaitovich, Philipp; Vogel, Jörg; Stadler, Peter F.; Hackermüller, Jörg (2009).
6950:
Sandes, Edans F. de O.; de Melo, Alba Cristina M.A. (May 2013). "Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU".
3095:
1101:
Protein sequence to structure alignment that includes secondary structure, structural conservation, structure-derived sequence profiles, and consensus alignment scores
5276:
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.
5980:-based algorithms like BWA and Bowtie. Supports up to 7 mismatches and/or indels with no performance penalty. Produces sensitive Smith–Waterman gapped alignments.
5828:
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
4054:
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.
3944:
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
4784:
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.
5293:
155:
Sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH. Position-specific iterative version CSI-BLAST more sensitive than PSI-BLAST
8008:
Marco-Sola, Santiago; Sammeth, Michael; GuigĂł, Roderic; Ribeca, Paolo (2012). "The GEM mapper: fast, accurate and versatile alignment by filtration".
6872:
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W; Kent; Smit; Zhang; Baertsch; Hardison; Haussler; Miller (2003).
5727:. 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.
140:
7353:
6921:
6141:
124:
3184:
3145:
8673:
Li, R.; Yu, C.; Li, Y.; Lam, T.-W.; Yiu, S.-M.; Kristiansen, K.; Wang, J. (2009). "SOAP2: an improved ultrafast tool for short read alignment".
8224:
Rivals, Eric; Salmela, Leena; Kiiskinen, Petteri; Kalsi, Petri; Tarhio, Jorma (2009). "Mpscan: Fast Localisation of Multiple Reads in Genomes".
3358:
Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. Able to recognize and separate gene duplications.
132:
128:
136:
259:
Genoogle uses indexing and parallel processing techniques for searching DNA and Proteins sequences. It is developed in Java and open source.
4982:
6078:
653:
112:
17:
5009:
multiple alignments per read. Use of ambiguous IUPAC codes in reference for common SNPs can improve SNP recall and remove allelic bias.
2336:
8951:
7308:
Rasmussen K, Stoye J, Myers EW; Stoye; Myers (2006). "Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length".
6098:
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ; Gish; Miller; Myers; Lipman (October 1990). "Basic local alignment search tool".
2531:
1214:
2207:
Multi-alignment; Full automatic sequence alignment; Automatic ambiguity correction; Internal base caller; Command line seq alignment
4949:
3824:
634:
395:
Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster
8059:
Clement, N. L.; Snell, Q.; Clement, M. J.; Hollenhorst, P. C.; Purwar, J.; Graves, B. J.; Cairns, B. R.; Johnson, W. E. (2009).
6871:
6770:"An energy-aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures"
8259:
7218:
6559:
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Giusti, Armando E. De; Naiouf, Marcelo; Prieto-Matias, Manuel (2016-06-30).
6325:
4929:
MOM or maximum oligonucleotide mapping is a query matching tool that captures a maximal length match within the short read.
658:
First parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences
4681:
533:
profile construction strategy to find distantly related protein sequences, and preventing homologous over-extension errors.
6825:
Rucci, Enzo; GarcĂa, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-MatĂas, Manuel (2015-12-25).
6768:
Rucci, Enzo; GarcĂa, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-MatĂas, Manuel (2015-12-25).
5581:
Indexes the reference genome as of version 2. Uses masks to generate possible keys. Can map ABI SOLiD color space reads.
639:
First parallelized algorithm employing the emerging Intel Xeon Phis to accelerate Smith-Waterman protein database search
6827:"SWIMM 2.0: enhanced Smith-Waterman on Intel's Multicore and Manycore architectures based on AVX-512 vector extensions"
4958:
algorithm seeded by results from a k-mer hashing scheme. Supports reads ranging in size from very short to very long.
7467:
Wilton, Richard; Budavari, Tamas; Langmead, Ben; Wheelan, Sarah J.; Salzberg, Steven L.; Szalay, Alexander S. (2015).
7004:. Proceedings of the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. pp. 383–384.
5346:
3906:(FM-index) short read alignment program based on BWA, supports alignment of indels with gap openings and extensions.
3621:
2071:
2413:
Progressive-iterative alignment. Multiple alignment of coding sequences accounting for frameshifts and stop codons.
7234:
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Naiouf, Marcelo; De Giusti,Armando; Prieto-Matias, Manuel (2018).
583:
Linking and profiling sequence alignment data from NCBI-BLAST results with major sequence analysis servers/services
499:
7025:"Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection"
2760:
Progressive-iterative-consistency-homology-extended alignment with preprofiling and secondary structure prediction
8946:
341:
8589:
Malhis, Nawar; Jones, Steven J. M. (2010). "High Quality SNP Calling Using Illumina Data at Shallow Coverage".
4487:
Extended Randomized Numerical alignEr for accurate alignment of NGS reads. It can map bisulfite-treated reads.
8118:"HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis"
3540:
Motif search and discovery (can get also positive & negative sequences as input for enriched motif search)
973:
Align chromatogram files (.ab1, .scf) against a template sequence, locate errors, and correct them instantly.
7164:
Li, M.; Ma, B.; Kisman, D.; Tromp, J. (2004). "Patternhunter II: highly sensitive and fast homology search".
5977:
4156:
4117:
3903:
40:
7469:"Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space"
7285:
Rucci, Enzo; Garcia, Carlos; Botella, Guillermo; Naiouf, Marcelo; De Giusti,Armando; Prieto-Matias, Manuel.
6716:"ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis"
1033:
Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ).
242:
Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ).
8116:
Santana-Quintero, Luis; Dingerdissen, Hayley; Thierry-Mieg, Jean; Mazumder, Raja; Simonyan, Vahan (2014).
8061:"The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing"
6981:. Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on. p. 160.
692:
Enhanced Smith-Waterman on Intel's Multicore and Manycore architectures based on AVX-512 vector extensions
8542:"Slider – Maximum use of probability information for alignment of short sequence reads and SNP detection"
8440:
Rumble, Stephen M.; Lacroute, Phil; Dalca, Adrian V.; Fiume, Marc; Sidow, Arend; Brudno, Michael (2009).
5716:
5565:
4014:
3141:
2714:
2637:
2237:
2233:
1075:
36:
5958:
5895:
5743:
5701:
5674:
5436:
5405:
5375:
5319:
5262:
5165:
4884:
4857:
4565:
4503:
4419:
4389:
4358:
4326:
4207:
4175:
4111:
4038:
3998:
3929:
3172:
3127:
3091:
2312:
2304:
2153:
1984:
1904:
7855:"CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform"
6503:
5521:
Up to 5 mixed substitutions and insertions-deletions; various tuning options and input-output formats
7074:"Back-translation for discovering distant protein homologies in the presence of frameshift mutations"
5829:
5118:
sensitivity, makes the Variant Toolkit well-suited for targeted sequencing projects and diagnostics.
7322:
7289:. 5th International Work-Conference on Bioinformatics and Biomedical Engineering. pp. 500–511.
4981:
Fast aligner based on a filtration strategy (no indexing, use q-grams and Backward Nondeterministic
8242:
6560:
3462:
A program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns
8375:"Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures"
7178:
7000:
Sandes, Edans F. de O.; Miranda, G.; De Melo, A.C.M.A.; Martorell, X.; Ayguade, E. (August 2014).
4724:
Yes, also supports Illumina *_int.txt and *_prb.txt files with all 4 quality scores for each base
6097:
4159:
to create an index of the genome. It's a bit slower than Bowtie but allows indels in alignment.
8237:
7317:
7173:
6999:
6977:
Sandes, Edans F. de O.; Miranda, G.; De Melo, A.C.M.A.; Martorell, X.; Ayguade, E. (May 2014).
6976:
4581:
Ultra fast and comprehensive NGS read aligner with high precision and small storage footprint.
3945:
1347:
3347:
Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy.
2288:
Progressive alignment for extremely large protein families (hundreds of thousands of members)
2110:
COmparison of Multiple Protein sequence Alignments with assessment of Statistical Significance
8326:"PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds"
7347:
6915:
6135:
4073:
75:
6504:"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets"
3486:
An efficient aligner for assemblies with explicit guarantees, aligning reads without splices
8785:"Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads"
8729:
8453:
8386:
8229:
8129:
7531:
6056:
6025:
5995:
5921:
5844:
banded alignment filter. For fixed-length reads only, authors recommend SHRiMP2 otherwise.
5804:
5770:
5532:
5501:
5467:
5229:
5195:
5133:
5059:
5024:
4764:
4699:
4661:
4627:
4596:
4403:
Sensitive and accurate base-space and color-space short-read alignment with hybrid seeding
4235:
4094:
3206:
2012:
1873:
1078:
44:
7233:
6754:
6528:
6414:
6369:
6195:
5361:
short reads obtained from next-generation sequencing to a genome with circular structure.
8:
7796:"Adaptable probabilistic mapping of short reads using position specific scoring matrices"
6060:
5999:
5199:
5137:
5063:
4665:
4631:
4600:
4310:
A CUDA compatible short read aligner to large genomes based on Burrows–Wheeler transform
3320:
2132:
1406:
8733:
8457:
8390:
8233:
8133:
7535:
599:
Local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST
278:
Local and global search with profile Hidden Markov models, more sensitive than PSI-BLAST
8917:
8892:
8868:
8841:
8817:
8784:
8760:
8717:
8566:
8541:
8476:
8441:
8417:
8374:
8350:
8325:
8265:
8201:
8176:
8152:
8117:
8093:
8060:
8041:
7985:
7960:
7936:
7903:
7830:
7795:
7768:
7735:
7711:
7676:
7554:
7519:
7495:
7468:
7444:
7417:
7393:
7368:
7262:
7235:
7100:
7073:
7049:
7024:
6854:
6807:
6735:
6691:
6666:
6598:
6541:
6479:
6454:
6435:
6289:
6262:
6243:
6123:
2708:
1725:
Opensource Smith-Waterman for SSE/CUDA, Suffix array based repeats finder & dotplot
32:
7652:
7619:
7284:
7141:
7124:
6898:
6873:
6642:
6617:
6218:
Buchfink, Xie and Huson (2015). "Fast and sensitive protein alignment using DIAMOND".
6111:
8922:
8873:
8822:
8804:
8765:
8747:
8698:
8690:
8655:
8647:
8606:
8571:
8522:
8481:
8422:
8404:
8355:
8306:
8255:
8206:
8157:
8098:
8080:
8033:
8025:
7990:
7941:
7923:
7884:
7876:
7835:
7817:
7773:
7755:
7716:
7698:
7677:"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome"
7657:
7639:
7600:
7559:
7500:
7449:
7434:
7398:
7335:
7267:
7214:
7191:
7146:
7105:
7054:
6903:
6846:
6799:
6755:
SAM: sequence alignment and modeling software system. Technical report UCSC-CRL-99-11
6696:
6647:
6602:
6590:
6533:
6484:
6439:
6427:
6419:
6374:
6321:
6294:
6235:
6200:
6115:
3437:
Profiling sequence alignment data from NCBI-BLAST results with major servers-services
2954:
Combines DNA and Protein alignment, by back translating the protein alignment to DNA.
2078:
442:
378:
High performance local aligner compatible to BLAST, but much faster; supports SAM/BAM
284:
8908:
8686:
8642:
8625:
8602:
8557:
8540:
Malhis, Nawar; Butterfield, Yaron S. N.; Ester, Martin; Jones, Steven J. M. (2009).
8517:
8500:
8341:
8301:
8284:
8269:
8076:
7976:
7919:
7871:
7854:
7751:
7595:
7578:
6858:
6811:
6739:
6682:
6470:
6359:
6342:
6185:
6169:"Discriminative modelling of context-specific amino acid substitution probabilities"
6168:
6127:
437:
420:
8912:
8904:
8863:
8853:
8812:
8796:
8755:
8737:
8682:
8637:
8598:
8561:
8553:
8512:
8471:
8461:
8412:
8394:
8345:
8337:
8296:
8247:
8196:
8188:
8147:
8137:
8088:
8072:
8045:
8017:
7980:
7972:
7931:
7915:
7866:
7825:
7807:
7763:
7747:
7706:
7688:
7647:
7631:
7590:
7549:
7539:
7490:
7480:
7439:
7429:
7388:
7380:
7327:
7290:
7257:
7247:
7236:"SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences"
7183:
7136:
7095:
7085:
7044:
7036:
7005:
6982:
6959:
6893:
6885:
6838:
6789:
6781:
6727:
6686:
6678:
6637:
6629:
6580:
6572:
6523:
6515:
6474:
6466:
6409:
6401:
6364:
6354:
6284:
6274:
6247:
6227:
6190:
6180:
6107:
4273:
4140:
1682:
1296:
1253:
508:
432:
86:
6618:"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs"
6545:
8742:
8466:
8399:
8251:
8142:
7544:
7294:
7002:
Fine-grain Parallel Megabase Sequence Comparison with Multiple Heterogeneous GPUs
6949:
4954:
Fast gapped aligner and reference-guided assembler. Aligns reads using a banded
1785:
516:
102:
8499:
David, Matei; Dzamba, Misko; Lister, Dan; Ilie, Lucian; Brudno, Michael (2011).
8115:
6318:
Biological sequence analysis: probabilistic models of proteins and nucleic acids
4465:
Implemented by Illumina. Includes ungapped alignment with a finite read length.
7287:
Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA
6826:
6769:
6279:
6155:
4955:
3611:
1641:
Smith-Waterman Acceleration on Intel's FPGA with OpenCL for Long DNA Sequences
1598:
1339:
7252:
7187:
6842:
8940:
8808:
8751:
8694:
8651:
8408:
8084:
8029:
7927:
7880:
7821:
7812:
7759:
7702:
7693:
7643:
6850:
6803:
6633:
6594:
6576:
6423:
5724:
5663:
5091:
4134:
3992:
3919:
2875:
2844:
1377:
605:
8718:"SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data"
8716:
AbuĂn, JosĂ© M.; Pichel, Juan C.; Pena, Tomás F.; Amigo, Jorge (2016-05-16).
7331:
7009:
6561:"OSWALD: OpenCL Smith–Waterman on Altera's FPGA for Large Protein Databases"
4771:
for academic and noncommercial users registered to HIVE deployment instance
1994:
Java-based multiple sequence alignment editor with integrated analysis tools
1022:
K. Frousios, T. Flouri, C. S. Iliopoulos, K. Park, S. P. Pissis, G. Tischler
675:
Smith-Waterman implementation for Intel Multicore and Manycore architectures
80:
Local search with fast k-tuple heuristic (Basic Local Alignment Search Tool)
8926:
8877:
8826:
8769:
8702:
8659:
8610:
8575:
8526:
8485:
8426:
8359:
8310:
8210:
8161:
8102:
8037:
7994:
7945:
7888:
7839:
7794:
Kerpedjiev, Peter; Frellsen, Jes; Lindgreen, Stinus; Krogh, Anders (2014).
7777:
7720:
7661:
7604:
7563:
7504:
7453:
7402:
7339:
7271:
7195:
7150:
7109:
7058:
6986:
6979:
CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters
6907:
6700:
6537:
6488:
6431:
6378:
6313:
6298:
6239:
6204:
5720:
5603:
4915:
4451:
3964:
3887:
2506:
2459:
1951:
821:
609:
446:
292:
98:
8858:
8800:
8285:"NextGenMap: fast and accurate read mapping in highly polymorphic genomes"
8192:
7579:"BigBWA: approaching the Burrows–Wheeler aligner to Big Data technologies"
7090:
6963:
6731:
6651:
6119:
5486:
Can handle insertions, deletions, mismatches; uses enhanced suffix arrays
2885:
Progressive alignment/hidden Markov model/Secondary structure/3D structure
7384:
7040:
5552:
4872:
Ungapped alignment that takes into account quality scores for each base.
3607:
3473:
Gene finding, alignment, annotation (human-mouse homology identification)
1448:
1227:
512:
94:
90:
7307:
4543:
8433:
8283:
Sedlazeck, Fritz J.; Rescheneder, Philipp; von Haeseler, Arndt (2013).
8228:. Lecture Notes in Computer Science. Vol. 5724. pp. 246–260.
8021:
7736:"Fast and accurate short read alignment with Burrows–Wheeler transform"
6794:
6585:
6405:
6231:
4745:
4518:
Finds global alignments of short DNA sequences against large DNA banks
1354:
1276:
logarithmic and affine gap costs and explicit models of indel evolution
893:
DNA sequence alignment of unrestricted size in single or multiple GPUs
698:
Rucci E, GarcĂa C, Botella G, De Giusti A, Naiouf M and Prieto-MatĂas M
681:
Rucci E, GarcĂa C, Botella G, De Giusti A, Naiouf M and Prieto-MatĂas M
7675:
Langmead, Ben; Trapnell, Cole; Pop, Mihai; Salzberg, Steven L (2009).
7635:
7485:
6889:
172:
GPU accelerated Smith Waterman algorithm for multiple shared-host GPUs
6785:
6519:
5973:
4267:
3764:
Letunic, Copley, Schmidt, Ciccarelli, Doerks, Schultz, Ponting, Bork
3668:
3421:
2823:
2227:
530:
493:
468:
Rucci E, GarcĂa C, Botella G, De Giusti A, Naiouf M, Prieto-MatĂas M
350:
288:
6715:
6615:
31:
is a compilation of software tools and web portals used in pairwise
8276:
8175:
Kielbasa, S.M.; Wan, R.; Sato, K.; Horton, P.; Frith, M.C. (2011).
6616:
Altschul SF, Madden TL, Schäffer AA, et al. (September 1997).
6029:
5925:
5825:
5808:
5774:
5536:
5505:
5471:
5420:
A randomized Numerical Aligner for Accurate alignment of NGS reads
5233:
5028:
4768:
4703:
4239:
4098:
4079:
3210:
3103:
2851:
2016:
1963:
1877:
1121:
Multiple, non-overlapping, local similarity (same algorithm as SIM)
1070:
462:
OpenCL Smith-Waterman on Altera's FPGA for Large Protein Databases
308:
Pairwise comparison of profile Hidden Markov models; very sensitive
303:
150:
6263:"Sensitive protein alignments at tree-of-life scale using DIAMOND"
5942:
Visual interface both for Bowtie and BWA, and an embedded aligner
3413:
Search for ncRNAs in genomes by partition function local alignment
6260:
5841:
3279:
An ultra-fast tool to find relative absent words in genomic data
3188:
3149:
3070:
2241:
2105:
2046:
1343:
844:
8282:
7793:
6565:
International Journal of High Performance Computing Applications
5972:
FPGA-accelerated reference sequence alignment mapping tool from
1319:
C/C++/Python/Java SIMD dynamic programming library for SSE, AVX2
953:
Posterior based local extension with descriptive evolution model
362:
High-performance general purpose sequence similarity search tool
8533:
8492:
5857:
5594:
4530:
4264:
4018:
2828:
Probabilistic/consistency with partition function probabilities
1053:
Global:Global (GG), Global:Local (GL) alignment with statistics
227:
Global:Global (GG), Global:Local (GL) alignment with statistics
8058:
7520:"BFAST: An Alignment Tool for Large Scale Genome Resequencing"
2713:
A human computing framework for comparative genomics to solve
2266:
Energy Based Multiple Sequence Alignment for DNA Binding Sites
1968:
Tree+multi-alignment; probabilistic-Bayesian; joint estimation
7466:
6667:"PSI-Search: iterative HOE-reduced profile SSEARCH searching"
6664:
5937:
5021:
Multi-threading and MPI versions available with paid license
3976:
3426:
Profiling sequence alignment data with major servers/services
3153:
3135:
2491:
2435:
2366:
Quality control and filtering of multiple sequence alignments
1428:"align" command aligns sequence & applies it to structure
1350:
421:"Search and clustering orders of magnitude faster than BLAST"
273:
203:
8007:
3584:
Prediction of transmembrane helices and topology of proteins
8539:
8223:
7674:
6824:
6767:
5837:
5833:
5667:
5095:
5031:
single threaded version for academic and noncommercial use
3923:
3457:
1936:
622:
Smith-Waterman search, slower but more sensitive than FASTA
7369:"YASS: enhancing the sensitivity of DNA similarity search"
7125:"PatternHunter: faster and more sensitive homology search"
6391:
539:
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR
8842:"Designing efficient spaced seeds for SOLiD read mapping"
7789:
7787:
7577:
AbuĂn, J.M.; Pichel, J.C.; Pena, T.F.; Amigo, J. (2015).
7518:
Homer, Nils; Merriman, Barry; Nelson, Stanley F. (2009).
7366:
5192:
Multiprocessor-core, client-server installation possible
4826:
3325:
Alignment of rearranged genomes using 6 frame translation
8891:
Lin, H.; Zhang, Z.; Zhang, M.Q.; Ma, B.; Li, M. (2008).
8439:
7904:"Long read alignment based on maximal exact match seeds"
6558:
6311:
6166:
3638:
GPU accelerated MEME (v4.4.0) algorithm for GPU clusters
3048:
Bayesian co-estimation of alignment and phylogeny (MCMC)
8372:
7511:
6455:"Lambda: the local aligner for massive biological data"
6452:
6217:
4646:
resequencing projects, namely in a diagnostic setting.
1705:
Aligns nucleic acid sequences given a protein alignment
1141:
Standard Needleman-Wunsch dynamic programming algorithm
529:
Combining the Smith-Waterman search algorithm with the
7784:
6665:
Li W, McWilliam H, Goujon M, et al. (June 2012).
793:
M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest
212:-tuple heuristic, slower but more sensitive than BLAST
8884:
8833:
8501:"SHRiMP2: Sensitive yet Practical Short Read Mapping"
8498:
8442:"SHRiMP: Accurate Mapping of Short Color-space Reads"
8174:
8001:
7961:"GASSST: global alignment short sequence search tool"
6952:
IEEE Transactions on Parallel and Distributed Systems
6720:
IEEE Transactions on Parallel and Distributed Systems
6167:
Angermüller, C.; Biegert, A.; Söding, J. (Dec 2012).
4082:. Can handle one mismatch in initial alignment step.
3573:
Stochastic motif extraction by statistical likelihood
3448:
Pairwise global alignment of completed genome regions
3075:
Multiple alignment and secondary structure prediction
709:
Fast Smith-Waterman search using SIMD parallelization
498:
Position-specific iterative BLAST, local search with
479:
Fast Smith-Waterman search using SIMD parallelization
8715:
8317:
7668:
7576:
6774:
Concurrency and Computation: Practice and Experience
6502:
Steinegger, Martin; Soeding, Johannes (2017-10-16).
3391:
Local multiple alignments of genome-length sequences
8623:
7517:
7166:
Journal of Bioinformatics and Computational Biology
6757:(Report). University of California, Santa Cruz, CA.
2782:
Nonprogressive, maximum expected accuracy alignment
8624:Li, R.; Li, Y.; Kristiansen, K.; Wang, J. (2008).
8366:
6752:
6343:"Protein homology detection by HMM-HMM comparison"
4287:Short-read alignment error correction using GPUs.
3551:Ungapped motif identification from BLOCKS database
1483:F. Teichert, J. Minning, U. Bastolla, and M. Porto
189:BLASTX and BLASTP aligner based on double indexing
8839:
8776:
8324:Chen, Yangho; Souaiaia, Tade; Chen, Ting (2009).
8177:"Adaptive seeds tame genomic sequence comparison"
7852:
7071:
6501:
2185:Segment-based method for intraspecific alignments
1694:I. Longden (modified from G. Myers and W. Miller)
1621:Java applet demonstrating various algorithms from
1161:Waterman-Eggert local alignment (based on LALIGN)
195:Buchfink B, Xie C, Huson DH, Reuter K, Drost HG
8938:
8323:
8052:
7952:
6453:Hauswedell H, Singer J, Reinert K (2014-09-01).
3830:
3221:Adaptive pair-Hidden Markov Model based approach
2341:Progressive-Iterative alignment; ClustalW plugin
1888:manual alignment ; some software assistance
8890:
8626:"SOAP: short oligonucleotide alignment program"
8582:
7895:
7846:
7163:
7072:Girdea, M; Noe, L; Kucherov, G (January 2010).
6713:
3562:Extraction and identification of shorter motifs
1474:Alignment using predicted Connectivity Profiles
993:GPU-based dynamic programming with backtracking
8217:
7460:
1821:
764:Fast heuristic anchor based pairwise alignment
384:Hannes Hauswedell, Jochen Singer, Knut Reinert
8782:
8109:
7959:Rizk, Guillaume; Lavenier, Dominique (2010).
7853:Liu, Y.; Schmidt, B.; Maskell, D. L. (2012).
6831:International Journal of Parallel Programming
6320:. Cambridge, UK: Cambridge University Press.
4749:and more conservative eukaryotic alignments.
3818:
2083:Multi-alignment; ClustalW & Phrap support
1013:Does pairwise sequence alignment with one gap
7958:
7727:
7418:"Persistent minimal sequences of SARS-CoV-2"
7352:: CS1 maint: multiple names: authors list (
7022:
6920:: CS1 maint: multiple names: authors list (
6156:https://github.com/UTennessee-JICS/HPC-BLAST
6140:: CS1 maint: multiple names: authors list (
4373:GPU-accelerated CUSHAW2 short-read aligner.
3717:Multiple motif and regular expression search
3301:Pairwise global alignment with whole genomes
1537:Local similarity with varying gap treatments
511:, Madden TL, Schäffer AA, Zhang J, Zhang Z,
8588:
7415:
6753:Hughey, R.; Karplus, K.; Krogh, A. (2003).
6079:List of open source bioinformatics software
3684:Pattern generation for use with ScanProsite
2910:Iterative alignment (especially refinement)
2676:2007 (latest stable 2013, latest beta 2016)
2518:MegAlign Pro (Lasergene Molecular Biology)
1405:Stochastic partition function sampling via
1201:MegAlign Pro (Lasergene Molecular Biology)
401:Steinegger M, Mirdita M, Galiez C, Söding J
8840:Noe, L.; Girdea, M.; Kucherov, G. (2010).
7901:
7409:
7211:Algorithms on strings, trees and sequences
6937:Improved pairwise alignment of genomic DNA
6934:
6261:B Buchfink, K Reuter and HG Drost (2021).
4254:Short-read mapping using Hadoop MapReduce
8916:
8867:
8857:
8816:
8759:
8741:
8672:
8641:
8565:
8516:
8475:
8465:
8416:
8398:
8349:
8300:
8241:
8200:
8151:
8141:
8092:
7984:
7935:
7870:
7829:
7811:
7767:
7710:
7692:
7651:
7594:
7570:
7553:
7543:
7494:
7484:
7443:
7433:
7392:
7321:
7261:
7251:
7177:
7140:
7122:
7099:
7089:
7048:
6897:
6793:
6714:Oehmen, C.; Nieplocha, J. (August 2006).
6690:
6641:
6584:
6527:
6478:
6413:
6368:
6358:
6288:
6278:
6194:
6184:
3649:Discriminative motif discovery and search
3336:Fuzzy whole genome alignment and analysis
2615:Progressive dynamic programming alignment
784:Alignments for membrane protein sequences
436:
8666:
8617:
7733:
7611:
7208:
6340:
3825:List of alignment visualization software
3780:Raghava, Searle, Audley, Barber, Barton
3369:Multiple alignment of rearranged genomes
3312:Alignment of cDNA sequences to a genome.
1494:Parallel whole-genome synteny alignments
2976:Sequence alignment by genetic algorithm
2222:Commercial (some modules are freeware)
50:
14:
8939:
7620:"BLAT---The BLAST-Like Alignment Tool"
5824:For Illumina or ABI SOLiD reads, with
2738:Progressive structure aware alignment
1714:G. Williams (modified from B. Pearson)
664:Liu Y, Tran TT, Lauenroth F, Schmidt B
5910:De-novo assembler for Illumina reads
4191:with biased nucleotide compositions.
1170:I. Longden (modified from W. Pearson)
733:
418:
161:Angermueller C, Biegert A, Soeding J
7617:
7416:Pratas, Diogo; Silva, Jorge (2020).
7367:Noe L, Kucherov G; Kucherov (2005).
6874:"Human-mouse alignments with BLASTZ"
5759:Fast for a small number of variants
4682:National Center for Genome Resources
3706:Motif extraction and database search
3257:
3108:More sensitive progressive alignment
6032:for academic and noncommercial use
5928:for academic and noncommercial use
5811:for academic and noncommercial use
5777:for academic and noncommercial use
5551:Short read error correction with a
5539:for academic and noncommercial use
5236:for academic and noncommercial use
4706:for academic and noncommercial use
4242:for academic and noncommercial use
4101:for academic and noncommercial use
2428:2011 (latest version, v2.07 2023)
1880:for education, research, nonprofit
29:list of sequence alignment software
24:
7123:Ma, B.; Tromp, J.; Li, M. (2002).
6316:; Mitchison, Graeme, eds. (1998).
5288:No, multiple processes per search
2932:Alignment preserving non-heuristic
1745:Smith-Waterman dynamic programming
1181:explicit models of indel evolution
500:position-specific scoring matrices
25:
8963:
8893:"ZOOM! Zillions of oligos mapped"
3290:Synteny and comparative genomics
2804:Partial order/hidden Markov model
1002:W. Frohmberg, M. Kierzynka et al.
412:Ultra-fast sequence analysis tool
8952:Lists of bioinformatics software
8783:Lunter, G.; Goodson, M. (2010).
7310:Journal of Computational Biology
7078:Algorithms for Molecular Biology
6312:Durbin, Richard; Eddy, Sean R.;
5666:; SOAP3, SOAP3-dp need GPU with
5474:for individual investigator use
3507:
1081:implementation of Smith-Waterman
970:Genome Compiler Genome Compiler
502:, much more sensitive than BLAST
8709:
8168:
7360:
7301:
7278:
7227:
7202:
7157:
7142:10.1093/bioinformatics/18.3.440
7116:
7065:
7016:
6993:
6970:
6943:
6928:
6865:
6818:
6761:
6746:
6707:
6658:
6609:
6552:
6495:
5432:Multithreading and MPI-enabled
4729:Multithreading and MPI-enabled
4499:Multithreading and MPI-enabled
3738:
3660:Motif search and alignment tool
3016:1994 (most recent version 2002)
2747:D. DeBlasio, J Braund, S Zhang
2664:Progressive-iterative alignment
2642:Progressive-iterative alignment
2440:Progressive-iterative alignment
2137:Progressive-iterative alignment
178:Liu Y, Maskell DL and Schmidt B
7435:10.1093/bioinformatics/btaa686
7213:. Cambridge university press.
6529:11858/00-001M-0000-002E-1967-3
6446:
6415:11858/00-001M-0000-0015-8D56-A
6385:
6370:11858/00-001M-0000-0017-EC7A-F
6334:
6305:
6254:
6211:
6196:11858/00-001M-0000-0015-8D22-F
6160:
6148:
6091:
4905:Yes, for structural variation
4441:Yes, for structural variation
3287:ACT (Artemis Comparison Tool)
2791:S.M.E. Sahraeian and B.J. Yoon
2593:Dynamic programming-clustering
2580:Y. Liu, B. Schmidt, D. Maskell
1661:Fast Local Alignment Searching
1577:Fast pairwise global alignment
1574:SPA: Super pairwise alignment
824:Biostrings::pairwiseAlignment
566:Highly parallel Scalable BLAST
13:
1:
8909:10.1093/bioinformatics/btn416
8687:10.1093/bioinformatics/btp336
8643:10.1093/bioinformatics/btn025
8603:10.1093/bioinformatics/btq092
8558:10.1093/bioinformatics/btn565
8518:10.1093/bioinformatics/btr046
8342:10.1093/bioinformatics/btp486
8302:10.1093/bioinformatics/btt468
8077:10.1093/bioinformatics/btp614
7977:10.1093/bioinformatics/btq485
7920:10.1093/bioinformatics/bts414
7902:Liu, Y.; Schmidt, B. (2012).
7872:10.1093/bioinformatics/bts276
7752:10.1093/bioinformatics/btp324
7596:10.1093/bioinformatics/btv506
7023:Chivian, D; Baker, D (2006).
6683:10.1093/bioinformatics/bts240
6471:10.1093/bioinformatics/btu439
6360:10.1093/bioinformatics/bti125
6186:10.1093/bioinformatics/bts622
6112:10.1016/S0022-2836(05)80360-2
6084:
5646:SOAP, SOAP2, SOAP3, SOAP3-dp
3831:Short-read sequence alignment
3595:Local structure motif library
3402:Multiple alignment of genomes
2919:Y. Totoki (based on O. Gotoh)
2204:DNA Baser Sequence Assembler
1042:Hepperle D (www.sequentix.de)
438:10.1093/bioinformatics/btq461
248:Hepperle D (www.sequentix.de)
41:structural alignment software
8743:10.1371/journal.pone.0155461
8467:10.1371/journal.pcbi.1000386
8400:10.1371/journal.pcbi.1000502
8252:10.1007/978-3-642-04241-6_21
8226:Algorithms in Bioinformatics
8143:10.1371/journal.pone.0099033
7545:10.1371/journal.pone.0007767
7295:10.1007/978-3-319-56154-7_45
6100:Journal of Molecular Biology
5005:Novoalign & NovoalignCS
3785:Benchmark collection (2009)
2673:T. Wheeler and J. Kececioglu
2036:M. Brudno and B. Morgenstern
982:Genome Compiler Corporation
7:
7734:Li, H.; Durbin, R. (2009).
6072:
5733:Low quality bases trimming
5426:Low quality bases trimming
4587:Low quality bases trimming
4493:Low quality bases trimming
4165:Low quality bases trimming
4028:Low quality bases trimming
2191:Local (preferred) or Global
2169:Local (preferred) or Global
1977:BD Redelings and MA Suchard
1822:Multiple sequence alignment
1601:) alignment with statistics
1517:Various dynamic programming
962:A. K. Hudek and D. G. Brown
37:multiple sequence alignment
10:
8968:
8846:Advances in Bioinformatics
8446:PLOS Computational Biology
8379:PLOS Computational Biology
6280:10.1038/s41592-021-01101-x
6154:HPC-BLAST code repository
3819:Alignment viewers, editors
3695:Motif database search tool
3627:Motif discovery and search
3529:Motif search and discovery
3168:2010 (newest version 2020)
3123:2000 (newest version 2008)
2966:2003 (newest version 2005)
2772:1999 (latest version 2009)
2381:2010 (latest version 2015)
2356:2005 (latest version 2017)
2256:2004 (newest version 2017)
2219:2006 (latest version 2018)
2197:2005 (latest version 2008)
2175:2005 (latest version 2008)
2098:2003 (latest version 2009)
1980:2005 (latest version 2018)
1900:1994 (latest version 2007)
1526:M.S. Waterman and P. Hardy
325:Inverse Document Frequency
7253:10.1186/s12918-018-0614-6
7188:10.1142/S0219720004000661
6843:10.1007/s10766-018-0585-7
5978:Burrows–Wheeler transform
5458:Yes, for variant calling
4157:Burrows–Wheeler transform
4118:Burrows–Wheeler transform
3904:Burrows–Wheeler transform
3812:Van Walle, Lasters, Wyns
3772:Thompson, Plewniak, Poch
3249:protein or nucleotide. **
2941:S.H. Sze, Y. Lu, Q. Yang.
2856:Probabilistic/consistency
2686:Probabilistic-consistency
2160:DIALIGN-TX and DIALIGN-T
1110:D. Chivian & D. Baker
1039:Local, SemiGlobal, Global
999:Local, SemiGlobal, Global
899:Local, SemiGlobal, Global
7813:10.1186/1471-2105-15-100
7694:10.1186/gb-2009-10-3-r25
6577:10.1177/1094342016654215
1813:protein or nucleotide **
1670:K. Rasmussen, W. Gerlach
1325:Global, Ends-free, Local
933:Java-based dot-plot tool
7332:10.1089/cmb.2006.13.296
7010:10.1145/2555243.2555280
6341:Söding J (April 2005).
5723:framework running atop
5717:Burrows–Wheeler Aligner
4015:Burrows–Wheeler Aligner
3380:Multiple Genome Aligner
3183:VectorFriends Aligner,
2991:1996 (new version 1998)
2963:Wernersson and Pedersen
2469:Multi-alignment of RNAs
1790:Seeded pattern-matching
1382:Seeded pattern-matching
913:Web-based dot-plot tool
870:Seeded pattern-matching
208:Local search with fast
18:Burrows–Wheeler Aligner
8947:Genetics-related lists
7379:(suppl_2): W540–W543.
7373:Nucleic Acids Research
7209:Gusfield, Dan (1997).
7029:Nucleic Acids Research
6987:10.1109/CCGrid.2014.18
6634:10.1093/nar/25.17.3389
6622:Nucleic Acids Research
5508:for noncommercial use
3946:Joint Genome Institute
2232:linked DNA to Protein
1897:J. Blandy and K. Fogel
1799:L. Noe and G. Kucherov
1633:1997 (reference book)
1586:Shen, Yang, Yao, Hwang
1566:X. Huang and W. Miller
1546:X. Huang and W. Miller
942:M. Pagni and T. Junier
8801:10.1101/gr.111120.110
8193:10.1101/gr.113985.110
7091:10.1186/1748-7188-5-6
6964:10.1109/TPDS.2012.194
6732:10.1109/TPDS.2006.112
5599:Free, [[BSD licenses
5202:, free trial version
3731:protein or nucleotide
3500:protein or nucleotide
2957:DNA/Protein (special)
2725:McGill Bioinformatics
2496:Progressive alignment
2391:Progressive alignment
2052:Progressive alignment
1768:-tuple pairwise match
1434:Global (by selection)
1127:Local non-overlapping
729:protein or nucleotide
419:Edgar, R. C. (2010).
7618:Kent, W. J. (2002).
6508:Nature Biotechnology
6053:Yes (GUI), no (CLI)
3982:Waterman alignment.
3902:A GPGPU accelerated
3570:Gibbs motif sampler
3440:Nucleotide, peptide
3429:Nucleotide, peptide
2561:1989 (modified 1995)
2326:R. K. Bradley et al.
2163:Segment-based method
51:Database search only
45:structural alignment
8859:10.1155/2010/708501
8734:2016PLoSO..1155461A
8458:2009PLSCB...5E0386R
8391:2009PLSCB...5E0502H
8234:2009LNCS.5724..246R
8134:2014PLoSO...999033S
7536:2009PLoSO...4.7767H
7240:BMC Systems Biology
6935:Harris R S (2007).
5315:Yes, client-server
4684:(NCGR) in Alpheus.
4611:Geneious Assembler
4533:version 2 License.
4091:Yes, client-server
3001:Hidden Markov model
2571:Dynamic programming
2546:Dynamic programming
2216:Heracle BioSoft SRL
2027:Iterative alignment
1685:dynamic programming
1534:SIM, GAP, NAP, LAP
1407:dynamic programming
1402:ProbA (also propA)
1299:dynamic programming
1256:dynamic programming
1050:GGSEARCH, GLSEARCH
850:Dynamic programming
827:Dynamic programming
645:Liu Y and Schmidt B
586:Nucleotide, peptide
224:GGSEARCH, GLSEARCH
8022:10.1038/nmeth.2221
7800:BMC Bioinformatics
7385:10.1093/nar/gki478
7041:10.1093/nar/gkl480
6406:10.1038/nmeth.1818
6232:10.1038/nmeth.3176
4322:Yes (GPU enabled)
3847:Use FASTQ quality
3844:paired-end option
3801:PREFAB 4.0 (2005)
3769:BAliBASE 3 (2015)
3142:multiple alignment
2837:Roshan and Livesay
2715:multiple alignment
2317:Sequence annealing
2275:Salama, RA. et al.
2244:and Smith-Waterman
2234:multiple alignment
1941:Sequence annealing
1855:A-Bruijn alignment
734:Pairwise alignment
33:sequence alignment
8903:(21): 2431–2437.
8681:(15): 1966–1967.
8336:(19): 2514–2521.
8295:(21): 2790–2791.
8261:978-3-642-04240-9
8016:(12): 1185–1188.
7971:(20): 2534–2540.
7914:(18): i318–i324.
7865:(14): 1830–1837.
7746:(14): 1754–1760.
7636:10.1101/gr.229202
7486:10.7717/peerj.808
7428:(21): 5129–5132.
7220:978-0-521-58519-4
6890:10.1101/gr.809403
6780:(18): 5517–5537.
6677:(12): 1650–1651.
6514:(11): 1026–1028.
6327:978-0-521-62971-3
6070:
6069:
5872:Subread, Subjunc
5448:RTG Investigator
4296:Yes, GPU enabled
3816:
3815:
3754:PFAM 30.0 (2016)
3732:
3724:
3723:
3673:Motif search tool
3501:
3493:
3492:
3258:Genomics analysis
3254:
3242:
3241:
3213:for academic use
2297:Deorowicz et al.
2079:CodonCode Aligner
2033:Local (preferred)
1818:
1806:
1805:
1681:Memory-optimized
1618:Sequences Studio
1613:1981 (Algorithm)
1357:at protein level)
1133:1991 (algorithm)
773:Huang, Umbach, Li
730:
722:
721:
431:(19): 2460–2461.
16:(Redirected from
8959:
8931:
8930:
8920:
8888:
8882:
8881:
8871:
8861:
8837:
8831:
8830:
8820:
8780:
8774:
8773:
8763:
8745:
8713:
8707:
8706:
8670:
8664:
8663:
8645:
8621:
8615:
8614:
8597:(8): 1029–1035.
8586:
8580:
8579:
8569:
8537:
8531:
8530:
8520:
8511:(7): 1011–1012.
8496:
8490:
8489:
8479:
8469:
8437:
8431:
8430:
8420:
8402:
8370:
8364:
8363:
8353:
8321:
8315:
8314:
8304:
8280:
8274:
8273:
8245:
8221:
8215:
8214:
8204:
8172:
8166:
8165:
8155:
8145:
8128:(6): 1754–1760.
8113:
8107:
8106:
8096:
8056:
8050:
8049:
8005:
7999:
7998:
7988:
7956:
7950:
7949:
7939:
7899:
7893:
7892:
7874:
7850:
7844:
7843:
7833:
7815:
7791:
7782:
7781:
7771:
7731:
7725:
7724:
7714:
7696:
7672:
7666:
7665:
7655:
7615:
7609:
7608:
7598:
7574:
7568:
7567:
7557:
7547:
7515:
7509:
7508:
7498:
7488:
7464:
7458:
7457:
7447:
7437:
7413:
7407:
7406:
7396:
7364:
7358:
7357:
7351:
7343:
7325:
7305:
7299:
7298:
7282:
7276:
7275:
7265:
7255:
7231:
7225:
7224:
7206:
7200:
7199:
7181:
7161:
7155:
7154:
7144:
7120:
7114:
7113:
7103:
7093:
7069:
7063:
7062:
7052:
7020:
7014:
7013:
6997:
6991:
6990:
6974:
6968:
6967:
6958:(5): 1009–1021.
6947:
6941:
6940:
6932:
6926:
6925:
6919:
6911:
6901:
6869:
6863:
6862:
6822:
6816:
6815:
6797:
6786:10.1002/cpe.3598
6765:
6759:
6758:
6750:
6744:
6743:
6711:
6705:
6704:
6694:
6662:
6656:
6655:
6645:
6628:(17): 3389–402.
6613:
6607:
6606:
6588:
6556:
6550:
6549:
6531:
6520:10.1038/nbt.3988
6499:
6493:
6492:
6482:
6450:
6444:
6443:
6417:
6389:
6383:
6382:
6372:
6362:
6338:
6332:
6331:
6309:
6303:
6302:
6292:
6282:
6258:
6252:
6251:
6215:
6209:
6208:
6198:
6188:
6164:
6158:
6152:
6146:
6145:
6139:
6131:
6095:
5114:Variant Toolkit
4895:mrFAST, mrsFAST
3835:
3834:
3793:HOMSTRAD (2005)
3743:
3742:
3726:
3512:
3511:
3495:
3262:
3261:
3244:
3026:Manual alignment
2019:, must register
1950:A. Schwartz and
1838:Alignment type**
1826:
1825:
1808:
1683:Needleman-Wunsch
1627:Local and global
1624:Generic sequence
1557:Local similarity
1297:Needleman-Wunsch
1254:Needleman-Wunsch
1030:Genome Magician
856:Both + Ends-free
833:Both + Ends-free
750:Alignment type**
738:
737:
724:
450:
440:
239:Genome Magician
55:
54:
21:
8967:
8966:
8962:
8961:
8960:
8958:
8957:
8956:
8937:
8936:
8935:
8934:
8889:
8885:
8838:
8834:
8789:Genome Research
8781:
8777:
8728:(5): e0155461.
8714:
8710:
8671:
8667:
8622:
8618:
8587:
8583:
8538:
8534:
8497:
8493:
8452:(5): e1000386.
8438:
8434:
8385:(9): e1000502.
8371:
8367:
8322:
8318:
8281:
8277:
8262:
8222:
8218:
8181:Genome Research
8173:
8169:
8114:
8110:
8057:
8053:
8006:
8002:
7957:
7953:
7900:
7896:
7851:
7847:
7792:
7785:
7732:
7728:
7673:
7669:
7624:Genome Research
7616:
7612:
7575:
7571:
7516:
7512:
7465:
7461:
7414:
7410:
7365:
7361:
7345:
7344:
7323:10.1.1.465.2084
7306:
7302:
7283:
7279:
7246:(Suppl 5): 96.
7232:
7228:
7221:
7207:
7203:
7162:
7158:
7121:
7117:
7070:
7066:
7021:
7017:
6998:
6994:
6975:
6971:
6948:
6944:
6933:
6929:
6913:
6912:
6878:Genome Research
6870:
6866:
6823:
6819:
6766:
6762:
6751:
6747:
6712:
6708:
6663:
6659:
6614:
6610:
6557:
6553:
6500:
6496:
6465:(17): 349–355.
6451:
6447:
6390:
6386:
6339:
6335:
6328:
6310:
6306:
6259:
6255:
6216:
6212:
6165:
6161:
6153:
6149:
6133:
6132:
6096:
6092:
6087:
6075:
5715:Integrates the
5555:data structure
4676:GMAP and GSNAP
4527:Multithreading
3853:Multi-threaded
3833:
3821:
3809:SABmark (2004)
3777:Oxbench (2011)
3741:
3735:
3521:Sequence type*
3510:
3504:
3271:Sequence type*
3260:
3253:local or global
3251:Alignment type:
3200:BioFriends team
3197:Local or global
3162:Local or global
3114:Local or global
3081:Local or global
3007:Local or global
2982:Local or global
2960:Local or global
2938:Local or global
2916:Local or global
2862:Local or global
2810:Local or global
2722:Local or global
2670:Local or global
2648:Local or global
2599:Local or global
2552:Local or global
2528:Local or global
2446:Local or global
2372:Local or global
2347:Local or global
2272:Local or global
2250:Local or global
2213:Local or global
2172:A.R.Subramanian
2119:R.I. Sadreyev,
2089:Local or global
2058:Local or global
2024:CHAOS, DIALIGN
2000:Local or global
1824:
1817:local or global
1815:Alignment type:
1543:Local or global
1523:Local or global
1059:Global in query
736:
64:Sequence type*
53:
23:
22:
15:
12:
11:
5:
8965:
8955:
8954:
8949:
8933:
8932:
8897:Bioinformatics
8883:
8832:
8795:(6): 936–939.
8775:
8708:
8675:Bioinformatics
8665:
8636:(5): 713–714.
8630:Bioinformatics
8616:
8591:Bioinformatics
8581:
8546:Bioinformatics
8532:
8505:Bioinformatics
8491:
8432:
8365:
8330:Bioinformatics
8316:
8289:Bioinformatics
8275:
8260:
8243:10.1.1.156.928
8216:
8187:(3): 487–493.
8167:
8108:
8065:Bioinformatics
8051:
8010:Nature Methods
8000:
7965:Bioinformatics
7951:
7908:Bioinformatics
7894:
7859:Bioinformatics
7845:
7783:
7740:Bioinformatics
7726:
7681:Genome Biology
7667:
7630:(4): 656–664.
7610:
7589:(24): 4003–5.
7583:Bioinformatics
7569:
7510:
7459:
7422:Bioinformatics
7408:
7359:
7316:(2): 296–308.
7300:
7277:
7226:
7219:
7201:
7172:(3): 417–439.
7156:
7135:(3): 440–445.
7129:Bioinformatics
7115:
7064:
7015:
6992:
6969:
6942:
6927:
6884:(1): 103–107.
6864:
6837:(2): 296–317.
6817:
6760:
6745:
6726:(8): 740–749.
6706:
6671:Bioinformatics
6657:
6608:
6571:(3): 337–350.
6551:
6494:
6459:Bioinformatics
6445:
6400:(2): 173–175.
6394:Nature Methods
6384:
6347:Bioinformatics
6333:
6326:
6304:
6273:(4): 366–368.
6267:Nature Methods
6253:
6220:Nature Methods
6210:
6179:(24): 3240–7.
6173:Bioinformatics
6159:
6147:
6089:
6088:
6086:
6083:
6082:
6081:
6074:
6071:
6068:
6067:
6065:
6063:
6054:
6051:
6049:
6047:
6045:
6042:
6038:
6037:
6035:
6033:
6023:
6021:
6019:
6017:
6015:
6011:
6007:
6006:
6004:
6002:
5993:
5990:
5987:
5984:
5981:
5976:. Faster than
5970:
5966:
5965:
5963:
5961:
5955:
5952:
5949:
5946:
5943:
5940:
5934:
5933:
5931:
5929:
5919:
5917:
5915:
5913:
5911:
5908:
5904:
5903:
5901:
5899:
5892:
5889:
5886:
5883:
5880:
5873:
5869:
5868:
5865:
5863:
5860:
5854:
5851:
5848:
5845:
5822:
5818:
5817:
5814:
5812:
5802:
5799:
5796:
5793:
5790:
5787:
5783:
5782:
5780:
5778:
5768:
5766:
5764:
5762:
5760:
5757:
5756:SSAHA, SSAHA2
5753:
5752:
5749:
5747:
5740:
5737:
5734:
5731:
5728:
5713:
5709:
5708:
5706:
5704:
5698:
5695:
5693:
5691:
5689:
5686:
5682:
5681:
5679:
5677:
5671:
5660:
5659:Yes, SOAP3-dp
5657:
5654:
5651:
5647:
5643:
5642:
5639:
5637:
5635:
5632:
5629:
5626:
5623:
5619:
5615:
5614:
5611:
5607:
5606:]] derivative
5600:
5597:
5591:
5588:
5585:
5582:
5579:
5575:
5574:
5572:
5570:
5568:
5562:
5560:
5558:
5556:
5549:
5545:
5544:
5542:
5540:
5530:
5528:
5526:
5524:
5522:
5519:
5515:
5514:
5511:
5509:
5499:
5496:
5493:
5490:
5487:
5484:
5480:
5479:
5477:
5475:
5465:
5462:
5459:
5456:
5453:
5449:
5445:
5444:
5442:
5440:
5433:
5430:
5427:
5424:
5421:
5418:
5414:
5413:
5411:
5409:
5402:
5400:
5397:
5394:
5391:
5387:
5383:
5382:
5380:
5378:
5372:
5369:
5367:
5364:
5362:
5358:
5354:
5353:
5351:
5349:
5343:
5341:
5339:
5337:
5335:
5332:
5328:
5327:
5325:
5323:
5316:
5313:
5311:
5309:
5307:
5303:
5299:
5298:
5295:
5291:
5289:
5286:
5283:
5280:
5277:
5274:
5270:
5269:
5267:
5265:
5259:
5256:
5254:
5252:
5250:
5246:
5242:
5241:
5239:
5237:
5227:
5224:
5221:
5218:
5215:
5212:
5208:
5207:
5205:
5203:
5193:
5190:
5187:
5184:
5181:
5177:
5173:
5172:
5170:
5168:
5162:
5159:
5157:
5155:
5153:
5149:
5145:
5144:
5142:
5140:
5131:
5128:
5125:
5122:
5119:
5115:
5108:
5107:
5104:
5102:
5099:
5088:
5085:
5082:
5079:
5075:
5071:
5070:
5068:
5066:
5057:
5054:
5051:
5048:
5045:
5041:
5037:
5036:
5034:
5032:
5022:
5019:
5016:
5013:
5010:
5006:
5002:
5001:
4998:
4996:
4994:
4992:
4990:
4988:
4986:
4979:
4975:
4974:
4972:
4970:
4968:
4965:
4963:
4961:
4959:
4956:Smith-Waterman
4952:
4946:
4945:
4943:
4941:
4939:
4936:
4934:
4932:
4930:
4927:
4923:
4922:
4920:
4918:
4912:
4909:
4906:
4903:
4900:
4896:
4892:
4891:
4889:
4887:
4881:
4879:
4877:
4875:
4873:
4870:
4866:
4865:
4862:
4860:
4854:
4851:
4848:
4845:
4842:
4838:
4834:
4833:
4831:
4829:
4823:
4820:
4817:
4814:
4811:
4808:
4804:
4803:
4801:
4799:
4796:
4793:
4790:
4787:
4785:
4782:
4778:
4777:
4774:
4772:
4762:
4759:
4756:
4753:
4750:
4742:
4738:
4737:
4734:
4732:
4730:
4727:
4725:
4722:
4720:
4716:
4712:
4711:
4709:
4707:
4697:
4694:
4691:
4688:
4685:
4677:
4673:
4672:
4670:
4668:
4659:
4656:
4653:
4650:
4647:
4643:
4639:
4638:
4636:
4634:
4625:
4622:
4620:
4618:
4616:
4612:
4608:
4607:
4605:
4603:
4594:
4591:
4588:
4585:
4582:
4579:
4575:
4574:
4571:
4569:
4562:
4559:
4556:
4553:
4550:
4546:
4540:
4539:
4536:
4534:
4528:
4525:
4523:
4521:
4519:
4516:
4512:
4511:
4509:
4507:
4500:
4497:
4494:
4491:
4488:
4485:
4481:
4480:
4478:
4476:
4474:
4472:
4470:
4468:
4466:
4463:
4459:
4458:
4456:
4454:
4448:
4445:
4442:
4439:
4436:
4432:
4428:
4427:
4424:
4422:
4416:
4413:
4410:
4407:
4404:
4401:
4397:
4396:
4394:
4392:
4386:
4383:
4380:
4377:
4374:
4371:
4367:
4366:
4363:
4361:
4355:
4352:
4349:
4346:
4343:
4339:
4335:
4334:
4331:
4329:
4323:
4320:
4317:
4314:
4311:
4308:
4304:
4303:
4301:
4299:
4297:
4294:
4292:
4290:
4288:
4285:
4281:
4280:
4278:
4276:
4270:
4261:
4259:
4257:
4255:
4252:
4248:
4247:
4245:
4243:
4233:
4230:
4228:
4226:
4224:
4220:
4216:
4215:
4212:
4210:
4204:
4201:
4198:
4195:
4192:
4188:
4184:
4183:
4180:
4178:
4172:
4169:
4166:
4163:
4160:
4153:
4149:
4148:
4145:
4143:
4137:
4131:
4128:
4125:
4122:
4114:
4108:
4107:
4104:
4102:
4092:
4089:
4087:
4085:
4083:
4076:
4070:
4069:
4067:
4065:
4063:
4061:
4059:
4057:
4055:
4052:
4048:
4047:
4044:
4042:
4035:
4032:
4029:
4026:
4023:
4011:
4007:
4006:
4003:
4001:
3995:
3989:
3987:
3985:
3983:
3979:
3973:
3972:
3969:
3967:
3961:
3958:
3955:
3952:
3949:
3941:
3937:
3936:
3934:
3932:
3926:
3916:
3913:
3910:
3907:
3900:
3896:
3895:
3892:
3890:
3884:
3881:
3878:
3875:
3872:
3868:
3864:
3863:
3860:
3857:
3854:
3851:
3848:
3845:
3842:
3839:
3832:
3829:
3820:
3817:
3814:
3813:
3810:
3806:
3805:
3802:
3798:
3797:
3794:
3790:
3789:
3786:
3782:
3781:
3778:
3774:
3773:
3770:
3766:
3765:
3762:
3758:
3757:
3755:
3751:
3750:
3747:
3740:
3737:
3729:Sequence type:
3722:
3721:
3718:
3715:
3711:
3710:
3707:
3704:
3700:
3699:
3696:
3693:
3689:
3688:
3685:
3682:
3678:
3677:
3674:
3671:
3665:
3664:
3661:
3658:
3654:
3653:
3650:
3647:
3643:
3642:
3639:
3636:
3632:
3631:
3628:
3625:
3618:
3617:
3614:
3612:Leucine Zipper
3606:Prediction of
3604:
3600:
3599:
3596:
3593:
3589:
3588:
3585:
3582:
3578:
3577:
3574:
3571:
3567:
3566:
3563:
3560:
3556:
3555:
3552:
3549:
3545:
3544:
3541:
3538:
3534:
3533:
3530:
3527:
3523:
3522:
3519:
3516:
3509:
3506:
3498:Sequence type:
3491:
3490:
3487:
3484:
3480:
3479:
3477:
3474:
3471:
3467:
3466:
3463:
3460:
3453:
3452:
3449:
3446:
3445:Shuffle-LAGAN
3442:
3441:
3438:
3435:
3431:
3430:
3427:
3424:
3418:
3417:
3414:
3411:
3407:
3406:
3403:
3400:
3396:
3395:
3392:
3389:
3385:
3384:
3381:
3378:
3374:
3373:
3370:
3367:
3363:
3362:
3359:
3356:
3352:
3351:
3348:
3345:
3341:
3340:
3337:
3334:
3330:
3329:
3326:
3323:
3317:
3316:
3313:
3310:
3306:
3305:
3302:
3299:
3295:
3294:
3291:
3288:
3284:
3283:
3280:
3277:
3273:
3272:
3269:
3266:
3259:
3256:
3247:Sequence type:
3240:
3239:
3237:
3234:
3228:
3225:
3222:
3219:
3215:
3214:
3204:
3201:
3198:
3195:
3192:
3181:
3180:VectorFriends
3177:
3176:
3169:
3166:
3163:
3160:
3157:
3138:
3132:
3131:
3124:
3121:
3115:
3112:
3109:
3106:
3100:
3099:
3088:
3085:
3082:
3079:
3076:
3073:
3067:
3066:
3064:
3061:
3055:
3052:
3049:
3046:
3042:
3041:
3039:
3036:
3033:
3030:
3027:
3024:
3020:
3019:
3017:
3014:
3008:
3005:
3002:
2999:
2995:
2994:
2992:
2989:
2983:
2980:
2977:
2974:
2970:
2969:
2967:
2964:
2961:
2958:
2955:
2952:
2948:
2947:
2945:
2942:
2939:
2936:
2933:
2930:
2926:
2925:
2923:
2922:1991 and later
2920:
2917:
2914:
2911:
2908:
2904:
2903:
2901:
2898:
2892:
2889:
2886:
2883:
2879:
2878:
2872:
2869:
2863:
2860:
2857:
2854:
2848:
2847:
2841:
2838:
2835:
2832:
2829:
2826:
2820:
2819:
2817:
2814:
2811:
2808:
2805:
2802:
2798:
2797:
2795:
2792:
2789:
2786:
2783:
2780:
2776:
2775:
2773:
2770:
2767:
2764:
2761:
2758:
2754:
2753:
2751:
2748:
2745:
2742:
2739:
2736:
2732:
2731:
2729:
2726:
2723:
2720:
2717:
2711:
2705:
2704:
2702:
2699:
2693:
2690:
2687:
2684:
2680:
2679:
2677:
2674:
2671:
2668:
2665:
2662:
2658:
2657:
2655:
2652:
2649:
2646:
2643:
2640:
2634:
2633:
2631:
2628:
2622:
2619:
2616:
2613:
2609:
2608:
2606:
2603:
2600:
2597:
2594:
2591:
2587:
2586:
2584:
2581:
2578:
2575:
2572:
2569:
2565:
2564:
2562:
2559:
2553:
2550:
2547:
2544:
2540:
2539:
2537:
2534:
2529:
2526:
2523:
2519:
2515:
2514:
2512:
2509:
2503:
2500:
2497:
2494:
2488:
2487:
2485:
2482:
2476:
2473:
2470:
2467:
2463:
2462:
2456:
2453:
2447:
2444:
2441:
2438:
2432:
2431:
2429:
2426:
2420:
2417:
2414:
2411:
2407:
2406:
2404:
2401:
2398:
2395:
2392:
2389:
2385:
2384:
2382:
2379:
2373:
2370:
2367:
2364:
2360:
2359:
2357:
2354:
2350:A.J. Drummond
2348:
2345:
2342:
2339:
2333:
2332:
2330:
2327:
2324:
2321:
2318:
2315:
2309:
2308:
2301:
2298:
2295:
2292:
2289:
2286:
2282:
2281:
2279:
2276:
2273:
2270:
2267:
2264:
2260:
2259:
2257:
2254:
2251:
2248:
2245:
2230:
2224:
2223:
2220:
2217:
2214:
2211:
2208:
2205:
2201:
2200:
2198:
2195:
2192:
2189:
2186:
2183:
2182:DNA Alignment
2179:
2178:
2176:
2173:
2170:
2167:
2164:
2161:
2157:
2156:
2150:
2147:
2146:Erik S. Wright
2144:
2141:
2138:
2135:
2129:
2128:
2126:
2123:
2117:
2114:
2111:
2108:
2102:
2101:
2099:
2096:
2092:P. Richterich
2090:
2087:
2084:
2081:
2075:
2074:
2068:
2065:
2059:
2056:
2053:
2050:
2043:
2042:
2040:
2037:
2034:
2031:
2028:
2025:
2021:
2020:
2010:
2007:
2001:
1998:
1995:
1992:
1988:
1987:
1981:
1978:
1975:
1972:
1969:
1966:
1960:
1959:
1957:
1954:
1948:
1945:
1942:
1939:
1933:
1932:
1929:
1926:
1923:
1920:
1917:
1913:
1909:
1908:
1901:
1898:
1895:
1892:
1889:
1886:
1882:
1881:
1871:
1868:
1862:
1859:
1856:
1853:
1849:
1848:
1845:
1842:
1839:
1836:
1835:Sequence type*
1833:
1830:
1823:
1820:
1811:Sequence type:
1804:
1803:
1800:
1797:
1794:
1791:
1788:
1782:
1781:
1778:
1775:
1772:
1769:
1763:
1759:
1758:
1755:
1752:
1749:
1746:
1743:
1739:
1738:
1735:
1732:
1729:
1726:
1723:
1719:
1718:
1715:
1712:
1709:
1706:
1703:
1699:
1698:
1695:
1692:
1689:
1686:
1679:
1675:
1674:
1671:
1668:
1665:
1662:
1659:
1655:
1654:
1651:
1648:
1645:
1642:
1639:
1635:
1634:
1631:
1628:
1625:
1622:
1619:
1615:
1614:
1611:
1608:
1605:
1602:
1599:Smith-Waterman
1595:
1591:
1590:
1587:
1584:
1581:
1578:
1575:
1571:
1570:
1567:
1564:
1561:
1558:
1555:
1551:
1550:
1547:
1544:
1541:
1538:
1535:
1531:
1530:
1527:
1524:
1521:
1518:
1515:
1511:
1510:
1507:
1503:M.G. Grabherr
1501:
1498:
1495:
1492:
1488:
1487:
1484:
1481:
1478:
1475:
1472:
1468:
1467:
1464:
1458:
1455:
1452:
1446:
1442:
1441:
1438:
1435:
1432:
1429:
1426:
1422:
1421:
1418:
1415:
1412:
1409:
1403:
1399:
1398:
1395:
1389:
1386:
1383:
1380:
1374:
1373:
1370:
1364:
1361:
1358:
1340:Smith-Waterman
1337:
1333:
1332:
1329:
1326:
1323:
1320:
1317:
1313:
1312:
1309:
1306:
1303:
1300:
1294:
1290:
1289:
1286:
1283:
1280:
1277:
1274:
1270:
1269:
1266:
1263:
1260:
1257:
1251:
1247:
1246:
1243:
1237:
1234:
1231:
1225:
1221:
1220:
1217:
1212:
1209:
1206:
1202:
1198:
1197:
1194:
1188:
1185:
1182:
1179:
1175:
1174:
1171:
1168:
1165:
1162:
1159:
1155:
1154:
1151:
1148:
1145:
1142:
1139:
1135:
1134:
1131:
1128:
1125:
1122:
1119:
1115:
1114:
1111:
1108:
1105:
1102:
1099:
1095:
1094:
1091:
1088:
1085:
1082:
1073:
1067:
1066:
1063:
1060:
1057:
1054:
1051:
1047:
1046:
1043:
1040:
1037:
1034:
1031:
1027:
1026:
1023:
1020:
1017:
1014:
1011:
1007:
1006:
1003:
1000:
997:
994:
991:
987:
986:
983:
980:
977:
974:
971:
967:
966:
963:
960:
957:
954:
951:
947:
946:
943:
940:
937:
934:
931:
927:
926:
923:
920:
917:
914:
911:
907:
906:
903:
900:
897:
894:
891:
887:
886:
883:
877:
874:
871:
868:
867:BLASTZ, LASTZ
864:
863:
860:
857:
854:
851:
848:
841:
840:
837:
834:
831:
828:
825:
818:
817:
814:
811:
808:
805:
802:
798:
797:
794:
791:
788:
785:
782:
778:
777:
774:
771:
768:
765:
762:
758:
757:
754:
751:
748:
747:Sequence type*
745:
742:
735:
732:
727:Sequence type:
720:
719:
716:
713:
710:
707:
703:
702:
699:
696:
693:
690:
686:
685:
682:
679:
676:
673:
669:
668:
665:
662:
659:
656:
650:
649:
646:
643:
640:
637:
631:
630:
628:
626:
623:
620:
616:
615:
612:
603:
600:
597:
593:
592:
589:
587:
584:
581:
577:
576:
573:
570:
567:
564:
560:
559:
556:
554:
551:
548:
544:
543:
540:
537:
534:
527:
523:
522:
519:
506:
503:
496:
490:
489:
486:
483:
480:
477:
473:
472:
469:
466:
463:
460:
456:
455:
452:
425:Bioinformatics
416:
413:
410:
406:
405:
402:
399:
396:
393:
389:
388:
385:
382:
379:
376:
372:
371:
368:
366:
363:
360:
356:
355:
353:
348:
345:
338:
334:
333:
331:
329:
326:
323:
319:
318:
315:
312:
309:
306:
300:
299:
296:
282:
279:
276:
270:
269:
266:
263:
260:
257:
253:
252:
249:
246:
243:
240:
236:
235:
233:
231:
228:
225:
221:
220:
218:
216:
213:
206:
200:
199:
196:
193:
190:
187:
183:
182:
179:
176:
173:
170:
166:
165:
162:
159:
156:
153:
147:
146:
143:
122:
119:
115:
109:
108:
105:
84:
81:
78:
72:
71:
68:
65:
62:
59:
52:
49:
9:
6:
4:
3:
2:
8964:
8953:
8950:
8948:
8945:
8944:
8942:
8928:
8924:
8919:
8914:
8910:
8906:
8902:
8898:
8894:
8887:
8879:
8875:
8870:
8865:
8860:
8855:
8851:
8847:
8843:
8836:
8828:
8824:
8819:
8814:
8810:
8806:
8802:
8798:
8794:
8790:
8786:
8779:
8771:
8767:
8762:
8757:
8753:
8749:
8744:
8739:
8735:
8731:
8727:
8723:
8719:
8712:
8704:
8700:
8696:
8692:
8688:
8684:
8680:
8676:
8669:
8661:
8657:
8653:
8649:
8644:
8639:
8635:
8631:
8627:
8620:
8612:
8608:
8604:
8600:
8596:
8592:
8585:
8577:
8573:
8568:
8563:
8559:
8555:
8551:
8547:
8543:
8536:
8528:
8524:
8519:
8514:
8510:
8506:
8502:
8495:
8487:
8483:
8478:
8473:
8468:
8463:
8459:
8455:
8451:
8447:
8443:
8436:
8428:
8424:
8419:
8414:
8410:
8406:
8401:
8396:
8392:
8388:
8384:
8380:
8376:
8369:
8361:
8357:
8352:
8347:
8343:
8339:
8335:
8331:
8327:
8320:
8312:
8308:
8303:
8298:
8294:
8290:
8286:
8279:
8271:
8267:
8263:
8257:
8253:
8249:
8244:
8239:
8235:
8231:
8227:
8220:
8212:
8208:
8203:
8198:
8194:
8190:
8186:
8182:
8178:
8171:
8163:
8159:
8154:
8149:
8144:
8139:
8135:
8131:
8127:
8123:
8119:
8112:
8104:
8100:
8095:
8090:
8086:
8082:
8078:
8074:
8070:
8066:
8062:
8055:
8047:
8043:
8039:
8035:
8031:
8027:
8023:
8019:
8015:
8011:
8004:
7996:
7992:
7987:
7982:
7978:
7974:
7970:
7966:
7962:
7955:
7947:
7943:
7938:
7933:
7929:
7925:
7921:
7917:
7913:
7909:
7905:
7898:
7890:
7886:
7882:
7878:
7873:
7868:
7864:
7860:
7856:
7849:
7841:
7837:
7832:
7827:
7823:
7819:
7814:
7809:
7805:
7801:
7797:
7790:
7788:
7779:
7775:
7770:
7765:
7761:
7757:
7753:
7749:
7745:
7741:
7737:
7730:
7722:
7718:
7713:
7708:
7704:
7700:
7695:
7690:
7686:
7682:
7678:
7671:
7663:
7659:
7654:
7649:
7645:
7641:
7637:
7633:
7629:
7625:
7621:
7614:
7606:
7602:
7597:
7592:
7588:
7584:
7580:
7573:
7565:
7561:
7556:
7551:
7546:
7541:
7537:
7533:
7530:(11): e7767.
7529:
7525:
7521:
7514:
7506:
7502:
7497:
7492:
7487:
7482:
7478:
7474:
7470:
7463:
7455:
7451:
7446:
7441:
7436:
7431:
7427:
7423:
7419:
7412:
7404:
7400:
7395:
7390:
7386:
7382:
7378:
7374:
7370:
7363:
7355:
7349:
7341:
7337:
7333:
7329:
7324:
7319:
7315:
7311:
7304:
7296:
7292:
7288:
7281:
7273:
7269:
7264:
7259:
7254:
7249:
7245:
7241:
7237:
7230:
7222:
7216:
7212:
7205:
7197:
7193:
7189:
7185:
7180:
7179:10.1.1.1.2393
7175:
7171:
7167:
7160:
7152:
7148:
7143:
7138:
7134:
7130:
7126:
7119:
7111:
7107:
7102:
7097:
7092:
7087:
7083:
7079:
7075:
7068:
7060:
7056:
7051:
7046:
7042:
7038:
7034:
7030:
7026:
7019:
7011:
7007:
7003:
6996:
6988:
6984:
6980:
6973:
6965:
6961:
6957:
6953:
6946:
6938:
6931:
6923:
6917:
6909:
6905:
6900:
6895:
6891:
6887:
6883:
6879:
6875:
6868:
6860:
6856:
6852:
6848:
6844:
6840:
6836:
6832:
6828:
6821:
6813:
6809:
6805:
6801:
6796:
6791:
6787:
6783:
6779:
6775:
6771:
6764:
6756:
6749:
6741:
6737:
6733:
6729:
6725:
6721:
6717:
6710:
6702:
6698:
6693:
6688:
6684:
6680:
6676:
6672:
6668:
6661:
6653:
6649:
6644:
6639:
6635:
6631:
6627:
6623:
6619:
6612:
6604:
6600:
6596:
6592:
6587:
6582:
6578:
6574:
6570:
6566:
6562:
6555:
6547:
6543:
6539:
6535:
6530:
6525:
6521:
6517:
6513:
6509:
6505:
6498:
6490:
6486:
6481:
6476:
6472:
6468:
6464:
6460:
6456:
6449:
6441:
6437:
6433:
6429:
6425:
6421:
6416:
6411:
6407:
6403:
6399:
6395:
6388:
6380:
6376:
6371:
6366:
6361:
6356:
6353:(7): 951–60.
6352:
6348:
6344:
6337:
6329:
6323:
6319:
6315:
6314:Krogh, Anders
6308:
6300:
6296:
6291:
6286:
6281:
6276:
6272:
6268:
6264:
6257:
6249:
6245:
6241:
6237:
6233:
6229:
6225:
6221:
6214:
6206:
6202:
6197:
6192:
6187:
6182:
6178:
6174:
6170:
6163:
6157:
6151:
6143:
6137:
6129:
6125:
6121:
6117:
6113:
6109:
6106:(3): 403–10.
6105:
6101:
6094:
6090:
6080:
6077:
6076:
6066:
6064:
6062:
6058:
6055:
6052:
6050:
6048:
6046:
6043:
6040:
6039:
6036:
6034:
6031:
6027:
6024:
6022:
6020:
6018:
6016:
6012:
6009:
6008:
6005:
6003:
6001:
5997:
5994:
5991:
5988:
5985:
5982:
5979:
5975:
5971:
5969:VelociMapper
5968:
5967:
5964:
5962:
5960:
5956:
5953:
5950:
5947:
5944:
5941:
5939:
5936:
5935:
5932:
5930:
5927:
5923:
5920:
5918:
5916:
5914:
5912:
5909:
5906:
5905:
5902:
5900:
5897:
5893:
5890:
5887:
5884:
5881:
5878:
5877:seed-and-vote
5874:
5871:
5870:
5866:
5864:
5861:
5859:
5855:
5852:
5849:
5846:
5843:
5839:
5835:
5831:
5827:
5823:
5820:
5819:
5815:
5813:
5810:
5806:
5803:
5800:
5797:
5794:
5791:
5788:
5785:
5784:
5781:
5779:
5776:
5772:
5769:
5767:
5765:
5763:
5761:
5758:
5755:
5754:
5750:
5748:
5745:
5741:
5738:
5735:
5732:
5729:
5726:
5722:
5718:
5714:
5711:
5710:
5707:
5705:
5703:
5699:
5696:
5694:
5692:
5690:
5687:
5684:
5683:
5680:
5678:
5676:
5672:
5669:
5665:
5664:POSIX Threads
5661:
5658:
5655:
5652:
5648:
5645:
5644:
5640:
5638:
5636:
5633:
5630:
5627:
5624:
5620:
5617:
5616:
5612:
5610:
5608:
5605:
5601:
5598:
5596:
5592:
5589:
5586:
5583:
5580:
5577:
5576:
5573:
5571:
5569:
5567:
5563:
5561:
5559:
5557:
5554:
5550:
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5546:
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5541:
5538:
5534:
5531:
5529:
5527:
5525:
5523:
5520:
5517:
5516:
5512:
5510:
5507:
5503:
5500:
5497:
5494:
5491:
5488:
5485:
5482:
5481:
5478:
5476:
5473:
5469:
5466:
5463:
5460:
5457:
5454:
5450:
5447:
5446:
5443:
5441:
5438:
5434:
5431:
5428:
5425:
5422:
5419:
5416:
5415:
5412:
5410:
5407:
5403:
5401:
5398:
5395:
5392:
5388:
5385:
5384:
5381:
5379:
5377:
5373:
5370:
5368:
5365:
5363:
5359:
5356:
5355:
5352:
5350:
5348:
5344:
5342:
5340:
5338:
5336:
5333:
5330:
5329:
5326:
5324:
5321:
5317:
5314:
5312:
5310:
5308:
5304:
5301:
5300:
5296:
5294:
5292:
5290:
5287:
5284:
5281:
5278:
5275:
5272:
5271:
5268:
5266:
5264:
5260:
5257:
5255:
5253:
5251:
5247:
5244:
5243:
5240:
5238:
5235:
5231:
5228:
5225:
5222:
5219:
5216:
5213:
5210:
5209:
5206:
5204:
5201:
5197:
5194:
5191:
5188:
5185:
5182:
5178:
5175:
5174:
5171:
5169:
5167:
5163:
5160:
5158:
5156:
5154:
5150:
5147:
5146:
5143:
5141:
5139:
5135:
5132:
5129:
5126:
5123:
5120:
5116:
5113:
5110:
5109:
5105:
5103:
5100:
5097:
5093:
5092:POSIX Threads
5089:
5086:
5083:
5080:
5076:
5073:
5072:
5069:
5067:
5065:
5061:
5058:
5055:
5052:
5049:
5046:
5042:
5039:
5038:
5035:
5033:
5030:
5026:
5023:
5020:
5017:
5014:
5011:
5007:
5004:
5003:
4999:
4997:
4995:
4993:
4991:
4989:
4987:
4984:
4980:
4977:
4976:
4973:
4971:
4969:
4966:
4964:
4962:
4960:
4957:
4953:
4951:
4948:
4947:
4944:
4942:
4940:
4937:
4935:
4933:
4931:
4928:
4925:
4924:
4921:
4919:
4917:
4913:
4910:
4907:
4904:
4901:
4897:
4894:
4893:
4890:
4888:
4886:
4882:
4880:
4878:
4876:
4874:
4871:
4868:
4867:
4863:
4861:
4859:
4855:
4852:
4849:
4846:
4843:
4839:
4836:
4835:
4832:
4830:
4828:
4824:
4821:
4818:
4815:
4812:
4809:
4806:
4805:
4802:
4800:
4797:
4794:
4791:
4788:
4786:
4783:
4780:
4779:
4775:
4773:
4770:
4766:
4763:
4760:
4757:
4754:
4751:
4747:
4743:
4741:HIVE-hexagon
4740:
4739:
4735:
4733:
4731:
4728:
4726:
4723:
4721:
4717:
4714:
4713:
4710:
4708:
4705:
4701:
4698:
4695:
4692:
4689:
4686:
4683:
4678:
4675:
4674:
4671:
4669:
4667:
4663:
4660:
4657:
4654:
4651:
4648:
4644:
4642:GensearchNGS
4641:
4640:
4637:
4635:
4633:
4629:
4626:
4623:
4621:
4619:
4617:
4613:
4610:
4609:
4606:
4604:
4602:
4598:
4595:
4592:
4589:
4586:
4583:
4580:
4578:Genalice MAP
4577:
4576:
4572:
4570:
4567:
4563:
4560:
4557:
4554:
4551:
4547:
4545:
4542:
4541:
4537:
4535:
4532:
4529:
4526:
4524:
4522:
4520:
4517:
4514:
4513:
4510:
4508:
4505:
4501:
4498:
4495:
4492:
4489:
4486:
4483:
4482:
4479:
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4471:
4469:
4467:
4464:
4461:
4460:
4457:
4455:
4453:
4449:
4446:
4443:
4440:
4437:
4433:
4430:
4429:
4425:
4423:
4421:
4417:
4414:
4411:
4408:
4405:
4402:
4399:
4398:
4395:
4393:
4391:
4387:
4384:
4381:
4378:
4375:
4372:
4369:
4368:
4364:
4362:
4360:
4356:
4353:
4350:
4347:
4344:
4340:
4337:
4336:
4332:
4330:
4328:
4324:
4321:
4318:
4315:
4312:
4309:
4306:
4305:
4302:
4300:
4298:
4295:
4293:
4291:
4289:
4286:
4283:
4282:
4279:
4277:
4275:
4271:
4269:
4266:
4262:
4260:
4258:
4256:
4253:
4250:
4249:
4246:
4244:
4241:
4237:
4234:
4231:
4229:
4227:
4225:
4221:
4218:
4217:
4213:
4211:
4209:
4205:
4202:
4199:
4196:
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4181:
4179:
4177:
4173:
4170:
4167:
4164:
4161:
4158:
4154:
4151:
4150:
4146:
4144:
4142:
4138:
4136:
4135:POSIX Threads
4132:
4129:
4126:
4123:
4119:
4115:
4113:
4110:
4109:
4105:
4103:
4100:
4096:
4093:
4090:
4088:
4086:
4084:
4081:
4077:
4075:
4072:
4071:
4068:
4066:
4064:
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4060:
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4053:
4050:
4049:
4045:
4043:
4040:
4036:
4033:
4030:
4027:
4024:
4020:
4016:
4012:
4009:
4008:
4004:
4002:
4000:
3996:
3994:
3993:POSIX Threads
3990:
3988:
3986:
3984:
3980:
3978:
3975:
3974:
3970:
3968:
3966:
3962:
3959:
3956:
3953:
3950:
3947:
3942:
3939:
3938:
3935:
3933:
3931:
3927:
3925:
3921:
3920:POSIX Threads
3917:
3914:
3911:
3908:
3905:
3901:
3898:
3897:
3893:
3891:
3889:
3885:
3882:
3879:
3876:
3873:
3869:
3866:
3865:
3861:
3858:
3855:
3852:
3849:
3846:
3843:
3840:
3837:
3836:
3828:
3826:
3811:
3808:
3807:
3803:
3800:
3799:
3795:
3792:
3791:
3787:
3784:
3783:
3779:
3776:
3775:
3771:
3768:
3767:
3763:
3761:SMART (2015)
3760:
3759:
3756:
3753:
3752:
3748:
3745:
3744:
3736:
3733:
3730:
3719:
3716:
3713:
3712:
3708:
3705:
3702:
3701:
3697:
3694:
3691:
3690:
3686:
3683:
3680:
3679:
3675:
3672:
3670:
3667:
3666:
3662:
3659:
3656:
3655:
3651:
3648:
3645:
3644:
3640:
3637:
3634:
3633:
3629:
3626:
3623:
3620:
3619:
3615:
3613:
3609:
3605:
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3601:
3597:
3594:
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3564:
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3558:
3557:
3553:
3550:
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3542:
3539:
3536:
3535:
3531:
3528:
3525:
3524:
3520:
3517:
3514:
3513:
3508:Motif finding
3505:
3502:
3499:
3488:
3485:
3482:
3481:
3478:
3475:
3472:
3469:
3468:
3464:
3461:
3459:
3455:
3454:
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3447:
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3439:
3436:
3433:
3432:
3428:
3425:
3423:
3420:
3419:
3415:
3412:
3409:
3408:
3404:
3401:
3398:
3397:
3393:
3390:
3387:
3386:
3382:
3379:
3376:
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3371:
3368:
3365:
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3357:
3354:
3353:
3349:
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3342:
3338:
3335:
3332:
3331:
3327:
3324:
3322:
3319:
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3314:
3311:
3308:
3307:
3303:
3300:
3297:
3296:
3292:
3289:
3286:
3285:
3281:
3278:
3275:
3274:
3270:
3267:
3264:
3263:
3255:
3252:
3248:
3238:
3235:
3233:
3229:
3226:
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3212:
3208:
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3199:
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3190:
3186:
3182:
3179:
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3155:
3151:
3147:
3143:
3139:
3137:
3134:
3133:
3129:
3125:
3122:
3120:
3117:C. Notredame
3116:
3113:
3110:
3107:
3105:
3102:
3101:
3097:
3093:
3089:
3086:
3083:
3080:
3077:
3074:
3072:
3069:
3068:
3065:
3062:
3060:
3056:
3053:
3050:
3047:
3044:
3043:
3040:
3037:
3034:
3031:
3028:
3025:
3022:
3021:
3018:
3015:
3013:
3009:
3006:
3003:
3000:
2997:
2996:
2993:
2990:
2988:
2985:C. Notredame
2984:
2981:
2978:
2975:
2972:
2971:
2968:
2965:
2962:
2959:
2956:
2953:
2950:
2949:
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2931:
2928:
2927:
2924:
2921:
2918:
2915:
2912:
2909:
2906:
2905:
2902:
2899:
2897:
2893:
2890:
2887:
2884:
2881:
2880:
2877:
2876:public domain
2873:
2870:
2868:
2864:
2861:
2858:
2855:
2853:
2850:
2849:
2846:
2845:public domain
2842:
2839:
2836:
2833:
2830:
2827:
2825:
2822:
2821:
2818:
2815:
2812:
2809:
2806:
2803:
2800:
2799:
2796:
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2790:
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2784:
2781:
2778:
2777:
2774:
2771:
2768:
2765:
2762:
2759:
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2755:
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2734:
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2730:
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2724:
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2718:
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2707:
2706:
2703:
2700:
2698:
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2675:
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2639:
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2399:
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2306:
2302:
2299:
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2277:
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2258:
2255:
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2249:
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2239:
2235:
2231:
2229:
2226:
2225:
2221:
2218:
2215:
2212:
2209:
2206:
2203:
2202:
2199:
2196:
2193:
2190:
2187:
2184:
2181:
2180:
2177:
2174:
2171:
2168:
2165:
2162:
2159:
2158:
2155:
2151:
2148:
2145:
2142:
2139:
2136:
2134:
2131:
2130:
2127:
2124:
2122:
2118:
2115:
2112:
2109:
2107:
2104:
2103:
2100:
2097:
2095:
2091:
2088:
2085:
2082:
2080:
2077:
2076:
2073:
2069:
2066:
2064:
2060:
2057:
2054:
2051:
2048:
2045:
2044:
2041:
2038:
2035:
2032:
2029:
2026:
2023:
2022:
2018:
2014:
2011:
2008:
2006:
2002:
1999:
1996:
1993:
1991:Base-By-Base
1990:
1989:
1986:
1982:
1979:
1976:
1973:
1971:Both + Codons
1970:
1967:
1965:
1962:
1961:
1958:
1955:
1953:
1949:
1946:
1943:
1940:
1938:
1935:
1934:
1930:
1927:
1924:
1921:
1918:
1914:
1911:
1910:
1906:
1902:
1899:
1896:
1893:
1890:
1887:
1884:
1883:
1879:
1875:
1872:
1869:
1867:
1863:
1860:
1857:
1854:
1851:
1850:
1846:
1843:
1840:
1837:
1834:
1831:
1828:
1827:
1819:
1816:
1812:
1801:
1798:
1795:
1792:
1789:
1787:
1784:
1783:
1779:
1776:
1773:
1770:
1767:
1764:
1761:
1760:
1756:
1753:
1750:
1747:
1744:
1741:
1740:
1736:
1733:
1730:
1727:
1724:
1721:
1720:
1716:
1713:
1710:
1707:
1704:
1701:
1700:
1696:
1693:
1690:
1687:
1684:
1680:
1677:
1676:
1672:
1669:
1666:
1663:
1660:
1657:
1656:
1652:
1649:
1646:
1643:
1640:
1637:
1636:
1632:
1629:
1626:
1623:
1620:
1617:
1616:
1612:
1609:
1606:
1603:
1600:
1596:
1593:
1592:
1588:
1585:
1582:
1579:
1576:
1573:
1572:
1568:
1565:
1562:
1559:
1556:
1553:
1552:
1548:
1545:
1542:
1539:
1536:
1533:
1532:
1528:
1525:
1522:
1519:
1516:
1513:
1512:
1508:
1506:
1502:
1499:
1496:
1493:
1490:
1489:
1485:
1482:
1479:
1476:
1473:
1470:
1469:
1465:
1463:
1459:
1456:
1453:
1450:
1447:
1444:
1443:
1439:
1436:
1433:
1430:
1427:
1424:
1423:
1419:
1416:
1413:
1410:
1408:
1404:
1401:
1400:
1396:
1394:
1390:
1387:
1384:
1381:
1379:
1378:PatternHunter
1376:
1375:
1371:
1369:
1365:
1362:
1359:
1356:
1352:
1349:
1345:
1341:
1338:
1335:
1334:
1330:
1327:
1324:
1321:
1318:
1315:
1314:
1310:
1308:A.C.R. Martin
1307:
1304:
1301:
1298:
1295:
1292:
1291:
1287:
1285:R. Cartwright
1284:
1281:
1278:
1275:
1272:
1271:
1267:
1264:
1261:
1258:
1255:
1252:
1249:
1248:
1244:
1242:
1238:
1235:
1232:
1229:
1226:
1223:
1222:
1218:
1216:
1213:
1210:
1207:
1203:
1200:
1199:
1195:
1193:
1189:
1186:
1183:
1180:
1177:
1176:
1172:
1169:
1166:
1163:
1160:
1157:
1156:
1152:
1149:
1146:
1143:
1140:
1137:
1136:
1132:
1129:
1126:
1123:
1120:
1117:
1116:
1112:
1109:
1106:
1103:
1100:
1097:
1096:
1092:
1089:
1086:
1083:
1080:
1077:
1074:
1072:
1069:
1068:
1064:
1061:
1058:
1055:
1052:
1049:
1048:
1044:
1041:
1038:
1035:
1032:
1029:
1028:
1024:
1021:
1018:
1015:
1012:
1009:
1008:
1004:
1001:
998:
995:
992:
989:
988:
984:
981:
978:
975:
972:
969:
968:
964:
961:
958:
955:
952:
949:
948:
944:
941:
938:
935:
932:
929:
928:
924:
921:
918:
915:
912:
909:
908:
904:
901:
898:
895:
892:
889:
888:
884:
882:
878:
875:
872:
869:
866:
865:
861:
858:
855:
852:
849:
846:
843:
842:
838:
835:
832:
829:
826:
823:
820:
819:
815:
812:
809:
806:
803:
800:
799:
795:
792:
789:
786:
783:
780:
779:
775:
772:
769:
766:
763:
760:
759:
755:
752:
749:
746:
743:
740:
739:
731:
728:
717:
714:
711:
708:
705:
704:
700:
697:
694:
691:
688:
687:
683:
680:
677:
674:
671:
670:
666:
663:
660:
657:
655:
652:
651:
647:
644:
641:
638:
636:
633:
632:
629:
627:
624:
621:
618:
617:
613:
611:
607:
604:
601:
598:
595:
594:
590:
588:
585:
582:
579:
578:
574:
572:Oehmen et al.
571:
568:
565:
562:
561:
557:
555:
552:
549:
546:
545:
541:
538:
535:
532:
528:
525:
524:
520:
518:
514:
510:
507:
504:
501:
497:
495:
492:
491:
487:
484:
481:
478:
475:
474:
470:
467:
464:
461:
458:
457:
453:
448:
444:
439:
434:
430:
426:
422:
417:
414:
411:
408:
407:
403:
400:
397:
394:
391:
390:
386:
383:
380:
377:
374:
373:
369:
367:
364:
361:
358:
357:
354:
352:
349:
346:
343:
339:
336:
335:
332:
330:
327:
324:
321:
320:
316:
313:
310:
307:
305:
302:
301:
297:
295:, Mitchison G
294:
290:
286:
283:
280:
277:
275:
272:
271:
267:
264:
261:
258:
255:
254:
250:
247:
244:
241:
238:
237:
234:
232:
229:
226:
223:
222:
219:
217:
214:
211:
207:
205:
202:
201:
197:
194:
191:
188:
185:
184:
180:
177:
174:
171:
168:
167:
163:
160:
157:
154:
152:
149:
148:
144:
142:
138:
134:
130:
126:
123:
120:
116:
114:
111:
110:
106:
104:
100:
96:
92:
88:
85:
82:
79:
77:
74:
73:
69:
66:
63:
60:
57:
56:
48:
47:of proteins.
46:
42:
38:
34:
30:
19:
8900:
8896:
8886:
8849:
8845:
8835:
8792:
8788:
8778:
8725:
8721:
8711:
8678:
8674:
8668:
8633:
8629:
8619:
8594:
8590:
8584:
8549:
8545:
8535:
8508:
8504:
8494:
8449:
8445:
8435:
8382:
8378:
8368:
8333:
8329:
8319:
8292:
8288:
8278:
8225:
8219:
8184:
8180:
8170:
8125:
8121:
8111:
8071:(1): 38–45.
8068:
8064:
8054:
8013:
8009:
8003:
7968:
7964:
7954:
7911:
7907:
7897:
7862:
7858:
7848:
7803:
7799:
7743:
7739:
7729:
7684:
7680:
7670:
7627:
7623:
7613:
7586:
7582:
7572:
7527:
7523:
7513:
7476:
7472:
7462:
7425:
7421:
7411:
7376:
7372:
7362:
7348:cite journal
7313:
7309:
7303:
7286:
7280:
7243:
7239:
7229:
7210:
7204:
7169:
7165:
7159:
7132:
7128:
7118:
7081:
7077:
7067:
7035:(17): e112.
7032:
7028:
7018:
7001:
6995:
6978:
6972:
6955:
6951:
6945:
6936:
6930:
6916:cite journal
6881:
6877:
6867:
6834:
6830:
6820:
6777:
6773:
6763:
6748:
6723:
6719:
6709:
6674:
6670:
6660:
6625:
6621:
6611:
6568:
6564:
6554:
6511:
6507:
6497:
6462:
6458:
6448:
6397:
6393:
6387:
6350:
6346:
6336:
6317:
6307:
6270:
6266:
6256:
6226:(1): 59–60.
6223:
6219:
6213:
6176:
6172:
6162:
6150:
6136:cite journal
6103:
6099:
6093:
6010:XpressAlign
5876:
5721:Apache Spark
5719:(BWA) on an
5609:
5357:REAL, cREAL
5176:Partek Flow
4680:Used by the
4370:CUSHAW2-GPU
3841:Description
3822:
3739:Benchmarking
3734:
3728:
3725:
3692:ScanProsite
3503:
3497:
3494:
3410:PLAST-ncRNA
3268:Description
3250:
3246:
3243:
3231:
3187:plugin, and
3118:
3094:3 (parte de
3058:
3011:
2986:
2895:
2866:
2696:
2625:
2612:Multi-LAGAN
2556:
2555:D.J. Lipman
2505:N. Bray and
2479:
2450:
2423:
2416:Nucleotides
2376:
2351:
2120:
2093:
2062:
2004:
1865:
1814:
1810:
1807:
1765:
1630:A.Meskauskas
1504:
1461:
1437:W. L. DeLano
1417:U. MĂĽckstein
1392:
1367:
1240:
1191:
880:
822:Bioconductor
726:
723:
428:
424:
209:
125:Burdyshaw CE
61:Description
28:
26:
8552:(1): 6–13.
6795:11336/53930
6586:11336/48798
6057:Proprietary
6026:Proprietary
5996:Proprietary
5922:Proprietary
5805:Proprietary
5771:Proprietary
5553:suffix tree
5533:Proprietary
5502:Proprietary
5468:Proprietary
5230:Proprietary
5196:Proprietary
5134:Proprietary
5074:NextGenMap
5060:Proprietary
5025:Proprietary
4765:Proprietary
4700:Proprietary
4662:Proprietary
4628:Proprietary
4597:Proprietary
4251:Cloudburst
4236:Proprietary
4095:Proprietary
3823:Please see
3676:Nucleotide
3608:Coiled coil
3543:Nucleotide
3518:Description
3489:Nucleotide
3476:Nucleotide
3465:Nucleotide
3451:Nucleotide
3416:Nucleotide
3405:Nucleotide
3394:Nucleotide
3383:Nucleotide
3372:Nucleotide
3361:Nucleotide
3350:Nucleotide
3339:Nucleotide
3328:Nucleotide
3315:Nucleotide
3304:Nucleotide
3293:Nucleotide
3282:Nucleotide
3207:Proprietary
2719:Nucleotides
2478:S. Siebert
2400:T. Lassmann
2269:Nucleotides
2210:Nucleotides
2086:Nucleotides
2013:Proprietary
1925:E. Wachtel
1891:Nucleotides
1874:Proprietary
1832:Description
1658:SWIFT suit
1471:SABERTOOTH
1449:suffix tree
1355:frameshifts
1348:translation
1228:suffix tree
1090:A. Moustafa
1079:open-source
976:Nucleotide
813:E. Wachtel
744:Description
563:ScalaBLAST
526:PSI-Search
509:Altschul SF
451:publication
141:Rekapalli B
87:Altschul SF
8941:Categories
8852:: 708501.
7806:(1): 100.
7687:(3): R25.
6085:References
6061:commercial
6000:commercial
5641:2009-2010
5613:2009-2011
5200:commercial
5148:PALMapper
5138:commercial
5064:commercial
4985:Matching)
4746:hash table
4666:commercial
4632:commercial
4601:commercial
4017:-BWA on a
3899:BarraCUDA
3859:Reference
3796:Mizuguchi
3703:TEIRESIAS
3657:PHI-Blast
3635:CUDA-MEME
3165:UGENE team
3148:, KAlign,
3045:StatAlign
3035:A. Rambaut
2907:PRRN/PRRP
2882:PROMALS3D
2769:J. Heringa
2624:M. Brudno
2507:L. Pachter
2422:V. Ranwez
2003:R. Brodie
1952:L. Pachter
1864:B.Raphael
1793:Nucleotide
1777:I. Longden
1762:wordmatch
1754:A. Bleasby
1708:Nucleotide
1702:tranalign
1678:stretcher
1673:2005,2008
1653:2017-2018
1644:Nucleotide
1610:W. Pearson
1580:Nucleotide
1454:Nucleotide
1397:2002–2004
1385:Nucleotide
1366:M. Gîrdea
1311:1990-2015
1265:A. Bleasby
1262:SemiGlobal
1233:Nucleotide
1219:1993-2016
1130:W. Pearson
1062:W. Pearson
1019:SemiGlobal
956:Nucleotide
916:Nucleotide
905:2011-2015
896:Nucleotide
885:2004,2009
873:Nucleotide
859:Y. M. Chan
836:P. Aboyoun
370:2009/2014
317:2005/2012
265:Albrecht F
198:2015/2021
181:2009/2010
8809:1088-9051
8752:1932-6203
8695:1367-4803
8652:1367-4803
8409:1553-7358
8238:CiteSeerX
8085:1367-4803
8030:1548-7091
7928:1367-4803
7881:1367-4803
7822:1471-2105
7760:1367-4803
7703:1465-6906
7644:1088-9051
7318:CiteSeerX
7174:CiteSeerX
6939:(Thesis).
6851:1573-7640
6804:1532-0634
6603:212680914
6595:1094-3420
6440:205420247
6424:1548-7105
5974:TimeLogic
5712:SparkBWA
5483:Segemehl
5094:, OpenCL/
5040:NextGENe
4268:MapReduce
4187:BWA-PSSM
4013:Runs the
3669:Phyloscan
3456:SIBsim4,
3434:Sequilab
3422:Sequerome
3140:Supports
3084:I. Holmes
3057:A. Novak
3010:A. Krogh
2951:RevTrans
2824:Probalign
2695:B. Paten
2602:F. Corpet
2590:MULTALIN
2568:MSAProbs
2536:1993-2023
2522:analysis.
2449:K. Katoh
2363:GUIDANCE
2253:DNADynamo
2228:DNADynamo
2061:Thompson
1912:ALLALIGN
1460:S. Kurtz
1353:(detects
1316:parasail
1239:S. Kurtz
1205:analysis.
1178:MCALIGN2
1138:NW-align
902:E. Sandes
890:CUDAlign
879:Schwartz
801:ALLALIGN
689:SWIMM2.0
654:SWAPHI-LS
606:Karplus K
580:Sequilab
531:PSI-BLAST
517:Lipman DJ
494:PSI-BLAST
476:parasail
337:Infernal
256:Genoogle
169:CUDASW++
133:Horton MD
113:HPC-BLAST
103:Lipman DJ
8927:18684737
8878:20936175
8827:20980556
8770:27182962
8722:PLOS ONE
8703:19497933
8660:18227114
8611:20190250
8576:18974170
8527:21278192
8486:19461883
8427:19750212
8360:19675096
8311:23975764
8270:17187140
8211:21209072
8162:24918764
8122:PLOS ONE
8103:19861355
8038:23103880
7995:20739310
7946:22962447
7889:22576173
7840:24717095
7778:19451168
7721:19261174
7662:11932250
7605:26323715
7564:19907642
7524:PLOS ONE
7505:25780763
7479:: e808.
7454:32730589
7403:15980530
7340:16597241
7272:30458766
7196:15359419
7151:11934743
7110:20047662
7084:(6): 6.
7059:16971460
6908:12529312
6859:49670113
6812:42945406
6740:11122366
6701:22539666
6538:29035372
6489:25161219
6432:22198341
6379:15531603
6299:33828273
6240:25402007
6205:23080114
6128:14441902
6073:See also
6030:freeware
5926:freeware
5809:freeware
5775:freeware
5670:support
5537:freeware
5506:freeware
5472:freeware
5234:freeware
5029:freeware
4769:freeware
4704:freeware
4400:CUSHAW3
4338:CUSHAW2
4284:CUDA-EC
4274:Artistic
4240:freeware
4141:Artistic
4099:freeware
4080:Jim Kent
4078:Made by
3856:License
3749:Authors
3698:Protein
3687:Protein
3616:Protein
3598:Protein
3592:I-sites
3587:Protein
3483:SRPRISM
3321:DECIPHER
3218:GLProbs
3211:freeware
3191:W plugin
3104:T-Coffee
2929:PSAlign
2852:ProbCons
2757:Praline
2735:PMFastR
2651:R. Edgar
2375:O. Penn
2337:Geneious
2291:Protein
2133:DECIPHER
2017:freeware
1964:BAli-Phy
1878:freeware
1847:License
1650:E. Rucci
1638:SWIFOLD
1594:SSEARCH
1491:Satsuma
1445:REPuter
1328:J. Daily
1190:J. Wang
1158:matcher
1071:JAligner
922:R. Bowen
847:dpAlign
781:AlignMe
715:Rognes T
619:SSEARCH
547:R&R
513:Miller W
465:Protein
447:20709691
409:USEARCH
392:MMseqs2
340:Profile
314:Söding J
304:HH-suite
285:Durbin R
186:DIAMOND
151:CS-BLAST
137:Brook RG
129:Sawyer S
99:Myers EW
95:Miller W
67:Authors
8918:2732274
8869:2945724
8818:3106326
8761:4868289
8730:Bibcode
8567:2638935
8477:2678294
8454:Bibcode
8418:2730575
8387:Bibcode
8351:2752623
8230:Bibcode
8202:3044862
8153:4053384
8130:Bibcode
8094:6276904
8046:2004416
7986:2951093
7937:3436841
7831:4021105
7769:2705234
7712:2690996
7555:2770639
7532:Bibcode
7496:4358639
7445:7559010
7394:1160238
7263:6245597
7101:2821327
7050:1635247
6692:3371869
6652:9254694
6480:4147892
6290:8026399
6248:5346781
6120:2231712
5907:Taipan
5842:AVX-512
5786:Stampy
5618:SLIDER
5578:SHRiMP
5518:SeqMap
5331:RazerS
5302:QPalma
5273:PRIMEX
4978:MPscan
4744:Uses a
4715:GNUMAP
4515:GASSST
4431:drFAST
4307:CUSHAW
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