List of sequence alignment software

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:

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; Guigó, 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; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, Manuel (2015-12-25).

6768:

Rucci, Enzo; García, Carlos; Botella, Guillermo; De Giusti, Armando; Naiouf, Marcelo; Prieto-Matías, 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:

Abuín, José 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, García C, Botella G, De Giusti A, Naiouf M and Prieto-Matías M

681:

Rucci E, García C, Botella G, De Giusti A, Naiouf M and Prieto-Matías 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, García C, Botella G, De Giusti A, Naiouf M, Prieto-Matías 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:

Abuín, 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: 5547: 5546: 5543: 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: 4477: 4475: 4473: 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: 4193: 4189: 4186: 4185: 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: 4062: 4060: 4058: 4056: 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: 3602: 3601: 3597: 3594: 3591: 3590: 3586: 3583: 3580: 3579: 3575: 3572: 3569: 3568: 3564: 3561: 3558: 3557: 3553: 3550: 3547: 3546: 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: 3450: 3447: 3444: 3443: 3439: 3436: 3433: 3432: 3428: 3425: 3423: 3420: 3419: 3415: 3412: 3409: 3408: 3404: 3401: 3398: 3397: 3393: 3390: 3387: 3386: 3382: 3379: 3376: 3375: 3371: 3368: 3365: 3364: 3360: 3357: 3354: 3353: 3349: 3346: 3343: 3342: 3338: 3335: 3332: 3331: 3327: 3324: 3322: 3319: 3318: 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: 3223: 3220: 3217: 3216: 3212: 3208: 3205: 3202: 3199: 3196: 3193: 3190: 3186: 3182: 3179: 3178: 3174: 3170: 3167: 3164: 3161: 3158: 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: 2946: 2943: 2940: 2937: 2934: 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: 2793: 2790: 2787: 2784: 2781: 2778: 2777: 2774: 2771: 2768: 2765: 2762: 2759: 2756: 2755: 2752: 2749: 2746: 2743: 2740: 2737: 2734: 2733: 2730: 2727: 2724: 2721: 2718: 2716: 2712: 2710: 2707: 2706: 2703: 2700: 2698: 2694: 2691: 2688: 2685: 2682: 2681: 2678: 2675: 2672: 2669: 2666: 2663: 2660: 2659: 2656: 2653: 2650: 2647: 2644: 2641: 2639: 2636: 2635: 2632: 2629: 2627: 2623: 2620: 2617: 2614: 2611: 2610: 2607: 2604: 2601: 2598: 2595: 2592: 2589: 2588: 2585: 2582: 2579: 2576: 2573: 2570: 2567: 2566: 2563: 2560: 2558: 2554: 2551: 2548: 2545: 2542: 2541: 2538: 2535: 2533: 2530: 2527: 2524: 2520: 2517: 2516: 2513: 2510: 2508: 2504: 2501: 2498: 2495: 2493: 2490: 2489: 2486: 2483: 2481: 2477: 2474: 2471: 2468: 2465: 2464: 2461: 2457: 2454: 2452: 2448: 2445: 2442: 2439: 2437: 2434: 2433: 2430: 2427: 2425: 2421: 2418: 2415: 2412: 2409: 2408: 2405: 2402: 2399: 2396: 2393: 2390: 2387: 2386: 2383: 2380: 2378: 2374: 2371: 2368: 2365: 2362: 2361: 2358: 2355: 2353: 2349: 2346: 2343: 2340: 2338: 2335: 2334: 2331: 2328: 2325: 2322: 2319: 2316: 2314: 2311: 2310: 2306: 2302: 2299: 2296: 2293: 2290: 2287: 2284: 2283: 2280: 2277: 2274: 2271: 2268: 2265: 2262: 2261: 2258: 2255: 2252: 2249: 2246: 2243: 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. Mückstein 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 4155:Uses a 4116:Uses a 4051:BLASTN 4010:BigBWA 3850:Gapped 3714:BASALT 3603:JCoils 3581:HMMTOP 3559:eMOTIF 3548:BLOCKS 3399:Multiz 3355:Splign 3276:EAGLE 3224:Protein 3189:Clustal 3156:plugins 3150:Clustal 3071:Stemloc 3004:Protein 2979:Protein 2913:Protein 2894:J. 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Ye 3227:Global 3185:MUSCLE 3171:Free, 3146:MUSCLE 3126:Free, 3119:et al. 3090:Free, 3059:et al. 3054:Global 3023:Se-Al 3012:et al. 2987:et al. 2896:et al. 2891:Global 2874:Free, 2867:et al. 2865:C. Do 2843:Free, 2834:Global 2813:C. Lee 2788:Global 2766:Global 2697:et al. 2692:Global 2683:Pecan 2638:MUSCLE 2626:et al. 2621:Global 2577:Global 2557:et al. 2502:Global 2480:et al. 2466:MARNA 2458:Free, 2451:et al. 2424:et al. 2410:MACSE 2397:Global 2377:et al. 2352:et al. 2323:Global 2303:Free, 2285:FAMSA 2238:MUSCLE 2152:Free, 2143:Global 2121:et al. 2116:Global 2094:et al. 2070:Free, 2063:et al. 2005:et al. 1983:Free, 1974:Global 1947:Global 1922:Local 1903:Free, 1866:et al. 1861:Global 1841:Author 1742:water 1734:UniPro 1722:UGENE 1691:Global 1583:Global 1505:et al. 1480:Global 1462:et al. 1425:PyMOL 1414:Global 1393:et al. 1391:B. 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