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speed-vs-accuracy-toolInfo2005-2020.tsv
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tool yearPublished journal impactFactor(2017) Journal H5-index(2017) totalCitations(2017) totalCitations(2020) H-index: (Corresponding author)(2017) M-index (Corresponding author)(2017) H (2020) M (2020) Versions Commits (Github) Contributers (Github) Issues Open Issues Closed Pull requests Forks Github repo fullCite
abyss 2009; 2009 Genome research; Bioinformatics 14.630 107 1410; 176 951 Inanc Birol:36 Inanc Birol:4.5 Inanc Birol:57 2.19 2.24 5475 29 9 287 78 86 https://github.com/bcgsc/abyss/ Simpson, Jared T., Kim Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven JM Jones, and Inanç Birol. "ABySS: a parallel assembler for short read sequence data." Genome research 19, no. 6 (2009): 1117-1123.; Birol, Inanç, Shaun D. Jackman, Cydney B. Nielsen, Jenny Q. Qian, Richard Varhol, Greg Stazyk, Ryan D. Morin et al. "De novo transcriptome assembly with ABySS." Bioinformatics 25, no. 21 (2009): 2872-2877.
adtex 2014 BMC Genomics NA NA NA 74 NA Saman K Halgamuge:46 1.59 2 NA NA NA NA NA NA NA Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, et al. Inferring copy number and genotype in tumour exome data. BMC Genomics. 2014;15:732.
angle NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
antepiseeker 2010 BMC research notes NA 38 34 115 NA NA NA NA 2 31 1 0 0 0 4 https://github.com/wyp1125/AntEpiSeeker2 Wang, Y., Liu, X., Robbins, K., & Rekaya, R. (2010). AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. BMC research notes, 3(1), 117.
apg 2008 BMC bioinformatics 2.576 74 166 317 Antti Airola:13 Antti Airola:1.86 Antti Airola:24 1.85 NA NA NA NA NA NA NA NA Airola, Antti, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, and Tapio Salakoski. "All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning." BMC bioinformatics 9, no. Suppl 11 (2008): S2.
arriba NA NA NA NA NA NA NA NA NA 1 374 2 1 125 1 23 https://github.com/suhrig/arriba NA
asgenseng 2015 Nucleic acids research NA NA NA 16 NA NA NA 1 NA NA NA NA NA NA NA Wang W, Wang W, Sun W, Crowley JJ, Szatkiewicz JP. Allele-specific copy-number discovery from whole-genome and whole-exome sequencing. Nucleic acids research. 2015 Aug 18;43(14):e90-.
baliphy 2006 Bioinformatics NA NA NA 255 NA Marc A. Suchard:80 3.48 3.5 14775 5 2 6 6 14 https://github.com/bredelings/BAli-Phy Suchard MA, Redelings BD. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics. 2006 Aug 15;22(16):2047-8.
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batalign 2015 Nucleic acids research NA NA NA 9 NA Wing-Kin Sung (宋永健):65 2.41 NA NA NA NA NA NA NA NA Lim JQ, Tennakoon C, Guan P, Sung WK. BatAlign: an incremental method for accurate alignment of sequencing reads. Nucleic acids research. 2015 Jul 13;43(16):e107-.
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bfast 2009 PloS one 3.234 161 400 645 Barry Merriman:43 Barry Merriman:2.39 Barry Merriman:51 1.65 1 1310 4 2 0 1 4 https://github.com/nh13/BFAST Homer, N., Merriman, B., & Nelson, S. F. (2009). BFAST: an alignment tool for large scale genome resequencing. PloS one, 4(11), e7767.
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bicseq 2011 Proceedings of the National Academy of Sciences 214 NA Peter J Park:101 5.05 1 NA NA NA NA NA NA NA Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proceedings of the National Academy of Sciences. 2011 Nov 15;108(46):E1128-36.
binpacker 2016 PLoS computational biology NA NA NA 86 NA Guojun Li:24 1.09 1 NA NA NA NA NA NA NA Liu J, Li G, Chang Z, Yu T, Liu B, McMullen R, Chen P, Huang X. BinPacker: packing-based de novo transcriptome assembly from RNA-seq data. PLoS computational biology. 2016 Feb 19;12(2):e1004772.
bismark 2011 Bioinformatics 4.900 106 329 2049 Felix Krueger:14 Felix Krueger:3.5 Felix Krueger:33 3.00 1.223 740 9 0 406 41 72 https://github.com/FelixKrueger/Bismark Krueger, Felix, and Simon R. Andrews. "Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications." Bioinformatics 27, no. 11 (2011): 1571-1572.
bismarkbowtiela 2011 Bioinformatics NA NA NA 2280 NA Felix Krueger:36 3.27 1.23 805 10 0 406 41 72 https://github.com/FelixKrueger/Bismark Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics. 2011 Jun 1;27(11):1571-2.
bismarkbowtielb 2011 Bioinformatics NA NA NA 2280 NA Felix Krueger:36 3.27 1.23 805 10 0 406 41 72 https://github.com/FelixKrueger/Bismark Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics. 2011 Jun 1;27(11):1571-2.
bismarkbowtielc 2011 Bioinformatics NA NA NA 2280 NA Felix Krueger:36 3.27 1.23 805 10 0 406 41 72 https://github.com/FelixKrueger/Bismark Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. bioinformatics. 2011 Jun 1;27(11):1571-2.
biss 2012 PloS one 3.234 161 9 28 Arndt von Haeseler:50 Arndt von Haeseler:2.38 Arndt von Haeseler:68 2.13 NA NA NA NA NA NA NA NA Dinh, Huy Q., Manu Dubin, Fritz J. Sedlazeck, Nicole Lettner, Ortrun Mittelsten Scheid, and Arndt von Haeseler. "Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis." PloS one 7, no. 7 (2012): e41528.
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bowtie 2009 Genome biology 10.800 83 6616 16949 Ben Langmead:13 Ben Langmead:2.17 Ben Langmead:29 2.64 1.3 2201 12 36 62 28 73 https://github.com/BenLangmead/bowtie Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25. doi:10.1186/gb-2009-10-3-r25
bowtie2 2012 Nature methods 32.072 125 2602 21420 Ben Langmead:13 Ben Langmead:2.17 Ben Langmead:29 2.64 2.41 2265 21 94 208 47 128 https://github.com/BenLangmead/bowtie2 Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357–9. doi:10.1038/nmeth.1923
bowtiestar 2009 Genome biology 10.800 83 6616 16949 Ben Langmead:13 Ben Langmead:2.17 Ben Langmead:29 2.64 1.3 2201 12 36 62 28 73 https://github.com/BenLangmead/bowtie Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25. doi:10.1186/gb-2009-10-3-r25
bratbw 2010 Bioinformatics 4.900 106 42 71 NA NA NA NA NA NA NA NA NA NA NA NA Harris, Elena Y., Nadia Ponts, Aleksandr Levchuk, Karine Le Roch, and Stefano Lonardi. "BRAT: bisulfite-treated reads analysis tool." Bioinformatics26, no. 4 (2010): 572-573.
breakdancer 2009 Nature methods NA NA NA 1295 NA NA NA 1.36 622 11 21 4 7 43 https://github.com/genome/breakdancer Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature methods. 2009 Sep;6(9):677-81.
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breakseq 2010 Nature biotechnology NA NA NA 199 NA Mark Gerstein:174 6.00 2 73 2 7 5 11 6 https://github.com/bioinform/breakseq2 Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature biotechnology. 2010 Jan;28(1):47-55.
bridger 2015 Genome biology 210 NA Zheng Chang:4 0.67 1.4 NA NA NA NA NA NA NA Chang Z, Li G, Liu J, Zhang Y, Ashby C, Liu D, Cramer CL, Huang X. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome biology. 2015 Dec 1;16(1):30.
bsmap 2009 BMC bioinformatics 2.576 74 167 646 Wei Li:43 Wei Li:3.31 Wei Li:74 3.89 NA NA NA NA NA NA NA NA Xi, Yuanxin, and Wei Li. "BSMAP: whole genome bisulfite sequence MAPping program." BMC bioinformatics 10, no. 1 (2009): 232.
bsmooth 2012 Genome Biology 10.800 83 119 452 Kasper D. Hansen:25; Ben Langmead:15; Rafael A Irizarry:62 Kasper D. Hansen:2.5; Ben Langmead:2.14; Rafael A Irizarry:4.77 Rafael A Irizarry:83 2.52 1 27 1 2 1 1 9 https://github.com/BenLangmead/bsmooth-align Hansen, K. D., Langmead, B., & Irizarry, R. A. (2012). BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol, 13(10), R83.
bsseeker 2010 BMC bioinformatics 2.576 74 137 226 matteo pellegrini:47 matteo pellegrini:2.94 matteo pellegrini:76 2.05 2.18 64 3 18 20 1 19 https://github.com/BSSeeker/BSseeker2 Chen, Pao-Yang, Shawn J. Cokus, and Matteo Pellegrini. "BS Seeker: precise mapping for bisulfite sequencing." BMC bioinformatics 11, no. 1 (2010): 203.
buckycon 2010 Bioinformatics 4.900 106 138 364 Cécile Ané:19 Cécile Ané:1.46 NA NA NA NA NA NA NA NA NA NA Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics, 26(22), 2910-2911.
buckymrbayes 2010 Bioinformatics 4.900 106 138 364 Cécile Ané:19 Cécile Ané:1.46 NA NA NA NA NA NA NA NA NA NA Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics, 26(22), 2910-2911.
buckymrbayesspa 2010 Bioinformatics 4.900 106 138 364 Cécile Ané:19 Cécile Ané:1.46 NA NA NA NA NA NA NA NA NA NA Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.Bioinformatics, 26(22), 2910-2911.
buckypop 2010 Bioinformatics 4.900 106 138 364 Cécile Ané:19 Cécile Ané:1.46 NA NA NA NA NA NA NA NA NA NA Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics, 26(22), 2910-2911.
buckyraxml 2010 Bioinformatics 4.900 106 138 364 Cécile Ané:19 Cécile Ané:1.46 NA NA NA NA NA NA NA NA NA NA Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.Bioinformatics, 26(22), 2910-2911.
builder 1994; 1995 Journal of molecular biology; Nature Structural & Molecular Biology 4.333; 13.309 62; 94 341; 100 423; 123 Patrice Koehl:38 Patrice Koehl:1.46 Patrice Koehl:44 1.42 NA NA NA NA NA NA NA NA Koehl, P., & Delarue, M. (1994). Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. Journal of molecular biology, 239(2), 249-275.; Koehl, P., & Delarue, M. (1995). A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nature Structural & Molecular Biology, 2(2), 163-170.
bwa 2009 Bioinformatics 4.900 106 6671 24863 Richard Durbin:104 Richard Durbin:4.95 Richard Durbin:135 3.97 1.717 931 23 133 88 110 485 https://github.com/lh3/bwa Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754–60. doi:10.1093/bioinformatics/btp324
bwamem 2009 Bioinformatics NA NA NA 26851 NA Richard Durbin:135 3.97 1.717 931 23 133 88 110 485 https://github.com/lh3/bwa Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. bioinformatics. 2009 Jul 15;25(14):1754-60.
bwapssm 2014 BMC bioinformatics NA NA NA 47 NA Anders Krogh:77 2.33 1.511 585 5 1 0 0 6 https://github.com/pkerpedjiev/bwa-pssm Kerpedjiev P, Frellsen J, Lindgreen S, Krogh A. Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC bioinformatics. 2014 Dec 1;15(1):100.
bwasw 2010 Bioinformatics 4.900 106 1731 6706 Richard Durbin:104 Richard Durbin:4.95 Richard Durbin:135 3.97 1.717 931 23 133 88 110 485 https://github.com/lh3/bwa Li, H., & Durbin, R. (2010). Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26(5), 589-595.
calista 2019 bioRxiv NA NA NA 4 NA Rudiyanto Gunawan:29 1.45 1 259 1 0 1 1 1 https://github.com/CABSEL/CALISTA Gao, N. P., Hartmann, T., Fang, T., & Gunawan, R. (2019). CALISTA: Clustering And Lineage Inference in Single-Cell Transcriptional Analysis. bioRxiv, 257550.
caml 2006 Systematic biology 14.387 57 58 90 Olivier Gascuel:36 Olivier Gascuel:2.25 Olivier Gascuel:45 1.32 NA NA NA NA NA NA NA NA Criscuolo, Alexis, Vincent Berry, Emmanuel JP Douzery, and Olivier Gascuel. "SDM: a fast distance-based approach for (super) tree building in phylogenomics." Systematic Biology 55, no. 5 (2006): 740-755.
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canu 2017 Genome research NA NA NA 1980 NA Adam M. Phillippy:45 2.50 2.1 10169 20 20 1940 43 159 https://github.com/marbl/canu Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome research. 2017 May 1;27(5):722-36.
canvas 2016 Bioinformatics NA NA NA 67 NA NA NA 1.4001613 1876 8 40 95 5 18 https://github.com/Illumina/canvas Roller E, Ivakhno S, Lee S, Royce T, Tanner S. Canvas: versatile and scalable detection of copy number variants. Bioinformatics. 2016 Aug 1;32(15):2375-7.
carma 2008 Nucleic acids research 9.100 172 226; 85 306; 137 Jens Stoye:42 Jens Stoye:2.33 Jens Stoye:46 1.35 3 6 2 0 0 0 0 https://github.com/wgerlach/CARMA3 Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A. and Stoye, J., 2008. Phylogenetic classification of short environmental DNA fragments. Nucleic acids research, 36(7), pp.2230-2239.; Gerlach, W. and Stoye, J., 2011. Taxonomic classification of metagenomic shotgun sequences with CARMA3. Nucleic acids research, p.gkr225.
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ce 1998 Protein engineering NA NA 1944 2365 Philip Bourne:54 Philip Bourne:3.6 Philip Bourne:73 1.46 NA NA NA NA NA NA NA NA Shindyalov, I. N., & Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein engineering, 11(9), 739-747.
celera 2008 Bioinformatics 4.900 106 321 547 NA NA NA NA NA NA NA NA NA NA NA NA Miller, Jason R., Arthur L. Delcher, Sergey Koren, Eli Venter, Brian P. Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark Mobarry, and Granger Sutton. "Aggressive assembly of pyrosequencing reads with mates."Bioinformatics 24, no. 24 (2008): 2818-2824.
cellrouter 2018 Nature communications NA NA NA 41 NA James J Collins:144 4.65 1 79 2 27 3 1 20 https://github.com/edroaldo/cellrouter Da Rocha EL, Rowe RG, Lundin V, Malleshaiah M, Jha DK, Rambo CR, Li H, North TE, Collins JJ, Daley GQ. Reconstruction of complex single-cell trajectories using CellRouter. Nature communications. 2018 Mar 1;9(1):1-3.
celltrails 2018 Cell reports NA NA NA 10 NA Peter G. Barr-Gillespie:51 1.59 1 158 5 0 2 0 2 https://github.com/dcellwanger/CellTrails Ellwanger DC, Scheibinger M, Dumont RA, Barr-Gillespie PG, Heller S. Transcriptional dynamics of hair-bundle morphogenesis revealed with CellTrails. Cell reports. 2018 Jun 5;23(10):2901-14.
celltreegibbs 2016 BMC bioinformatics NA NA NA 38 NA Koji Tsuda:44 1.69 1 NA NA NA NA NA NA NA Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC bioinformatics. 2016 Dec 1;17(1):363.
celltreemaptpx 2016 BMC bioinformatics NA NA NA 38 NA Koji Tsuda:44 1.69 1 NA NA NA NA NA NA NA Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC bioinformatics. 2016 Dec 1;17(1):363.
celltreevem 2016 BMC bioinformatics NA NA NA 38 NA Koji Tsuda:44 1.69 1 NA NA NA NA NA NA NA Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC bioinformatics. 2016 Dec 1;17(1):363.
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lmat 2013 Bioinformatics 4.981 106 29 167 Jonathan E Allen:15 Jonathan E Allen:1.15 Jonathan E Allen:24 1.33 1.24 86 2 5 6 1 2 https://github.com/LivGen/LMAT Ames, Sasha K., David A. Hysom, Shea N. Gardner, G. Scott Lloyd, Maya B. Gokhale, and Jonathan E. Allen. "Scalable metagenomic taxonomy classification using a reference genome database." Bioinformatics 29, no. 18 (2013): 2253-2260.
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qiime 2010 Nature methods 32.072 125 3432 21646 Rob Knight:95 Rob Knight:9.5 Rob Knight:187 8.50 1.91 7718 54 387 996 847 264 https://github.com/biocore/qiime Caporaso, J. Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello, Noah Fierer et al. "QIIME allows analysis of high-throughput community sequencing data." Nature methods 7, no. 5 (2010): 335-336.
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