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Table 1 Highly cited genomic software tools

From: Challenges in funding and developing genomic software: roots and remedies

Program name Yeara Primary institution(s)b Primary funding source(s)c Refs.d Citationse
Homology searching and alignment
 FASTA 1988 U. Virginia, NIH NA [15] 13,496
 CLUSTAL 1988 Trinity College, Dublin; EMBL, Heidelberg; EBI European Community Biotechnology Action Programme [16,17,18,19,20] 94,789
 BLAST 1990 NCBI NIH [21] 75,328
 PSI-BLAST 1997 NCBI NIH [22] 69,604
 HMMer 1998 Washington U., St. Louis NIH, HHMI [23,24,25] 8,836
 T-Coffee 2000 Nat. Inst. Med. Res., London Swiss Nat’l Science Fnd. [26] 6,247
 BLAT 2002 UC Santa Cruz NIH, HHMI [27] 6,911
 MUSCLE 2004 drive5.com NA [28] 24,261
 MAFFT 2013 Kyoto U. Ministry of Education, Culture, Sports, and Technology of Japan [29,30,31,32,33] 21,486
Phylogenetic modeling and tree inference
 PHYLIP 1980 U. Washington NIH, NSF [34] 21,851
 MacClade 1986 Sinauer Assoc. (Commercial) [35] 10,255
 PAUP 1989 Illinois Nat. Hist. Survey, Sinauer Assoc. (Commercial) [4] 62,807
 PAML 1993 UC Berkeley, Univ. College London NSF of China, NIH, NSF [36, 37] 11,375
 MEGA 1993 Penn. State U., Arizona State U. NIH, NSF, Burroughs-Wellcome [38,39,40,41,42] 119,268
 Mr. Bayes 2001 U. Rochester, Uppsala U. NSF [43,44,45] 52,742
 Mesquite 2001 U. Arizona, U. British Columbia Packard, NSF [46] 7,693
 PhyML 2003 CNRS, Montpellier Montpellier Genopole, InterEPST Bioinformatics Program [47,48,49,50] 24,614
 PHAST 2004 UC Santa Cruz, Cornell NSF, Packard, NIH [51,52,53,54,55] 4,690
 RAxML 2004 Technical U. Munich Heidelberg Institute for Theoretical Studies [56,57,58,59] 27,550
 HyPhy 2005 UC San Diego, NC State NA [60] 2,159
 BEAST 2007 U. Auckland, U. Edinburgh Wellcome Trust, Royal Society [61, 62] 12,027
 FastTree/FastTree2 2009 Lawrence Berkeley Nat’l Lab, UC Berkeley DOE, GTL Program [63, 64] 5,308
Gene prediction, motif finding, and RNA folding
 MEME 1994 UC San Diego NIH, NSF [65,66,67,68,69] 11,790
 Genscan 1997 Stanford NIH, NSF [70] 4,061
 tRNAscan-SE 1997 Washington U., St. Louis NA [71] 7,559
 Vienna package 2003 Institute for Theoretical Chemistry, Austria Austrian Science Fund [72,73,74] 4,781
Visualization
 Jalview 1996 EBI, Sanger, Oxford BBSRC [75, 76] 5,895
 TreeView 1998 Stanford NIH [77] 17,796
 UCSC Genome Browser 2000 UC Santa Cruz NIH, DOE, HHMI [78,79,80,81,82] 11,365
 ENSEMBL Browser 2000 EBI, Sanger Wellcome Trust, NIH, EMBL [83,84,85,86,87] 5,235
 Cytoscape 2003 Inst. Systems Biology, Whitehead Inst., UC San Diego Pfizer, NIH, NSF [88,89,90] 17,862
 IGV 2011 Broad NIH [91] 4,678
Statistical and population genomics
 STRUCTURE 2000 Oxford NIH, Burroughs-Wellcome, BBRC [92, 93] 30,948
 PHASE/fastPHASE 2001 Oxford, U. Washington Wellcome Trust, BBSRC, Engineering and Physical Sciences Research Council [94,95,96] 10,073
 ms 2002 U. Chicago NA [97] 2,119
 PolyPhen 2002 EMBL, Max Delbrück Center for Mol. Med., Engelhardt Inst. Mol. Biol. NIH [98,99,100] 11,136
 SIFT 2003 Fred Hutchinson Cancer Res. Ctr. NIH [101, 102] 7,024
 EIGENSTRAT 2006 Harvard, Broad Millenium Pharmaceuticals, Burroughs Wellcome [103] 6,812
 PLINK 2007 MGH, Broad, U. Hong Kong NIH [104, 105] 17,938
 TASSEL 2007 USDA-ARS, Cornell USDA-ARS, NSF [106] 2,609
 BEAGLE 2007 U. Auckland University of Auckland Research Committee, NIH [107, 108] 2,997
 IMPUTE/IMPUTE2 2007 Oxford Wellcome Trust, NIH [109, 110] 4,930
 VCFtools 2011 Sanger Medical Research Council, British Heart Foundation, Wellcome Trust, NIH [111] 3,133
 CADD 2014 U. Washington NIH [112] 2,353
Functional genomics, annotations, and transcriptomics
 Gene Ontology 2000 UC Berkeley, Stanford NIH, Astra Zeneca [113] 22,898
 GSEA 2005 Broad NA [114] 16,135
 MACS/MACS2 2008 Dana-Farber, Harvard NIH [115, 116] 5,965
 TopHat/Cufflinks 2009 U. Maryland NIH, NSF [117,118,119,120] 28,242
 ChromHMM 2010 MIT, Broad NSF, NIH [121,122,123] 3,977
 BEDtools 2010 U. Virginia NIH, Burroughs-Wellcome [124, 125] 7,137
 edgeR 2010 Garavan Inst. Med. Res., Walter & Eliza Hall Inst. Med. Res., Australia NHMRC [126] 9,992
 Trinity 2011 MIT, Broad NIH, US-Israel Binational Science Foundation [127] 7,178
 DEseq/DEseq2 2012 EMBL NA [128, 129] 16,355
Assembly, read mapping, and base/variant calling
 Staden package 1977 LMB NA [130,131,132,133,134] 5,029
 Phred 1993 Washington U., St. Louis, U. Washington NIH [135, 136] 12,172
 MAQ 2008 Sanger Wellcome Trust [137] 2,777
 ALLPATHS/ALLPATHS-LG 2008 Broad, MGH NIH [138, 139] 2,079
 Velvet 2008 EBI EMBL [140] 7,635
 Bowtie/Bowtie2 2009 U. Maryland NIH [141, 142] 26,607
 BWT 2009 Sanger Wellcome Trust [143] 17,546
 SOAP2 2009 Beijing Genomics Inst., U. Southern Denmark National Natural Science Foundation of China, Danish Natural Science Research Council [144] 2,818
 SAMtools 2009 Sanger Wellcome Trust, NIH [145] 17,811
 ABySS 2009 Genome Sciences Centre, Vancouver, BC Genome Canada, Genome British Columbia, British Columbia Cancer Foundation [146] 2,761
 GATK 2010 Broad, MGH NIH [147] 9,291
 SOAPdenovo/SOAPdenovo2 2010 Beijing Genomics Inst. Chinese Academy of Science, National Natural Science Foundation of China [148, 149] 4,295
 STAR 2013 CSHL NIH [150, 151] 6,013
  1. a Approximate first year available, or year of first publication if unknown
  2. bInstitutions most central in supporting project, or affiliations of first and last authors of first publication if unknown. Broad Eli & Edythe Broad Institute of MIT & Harvard, USA; CNRS Centre National de la Recherche Scientifique, France; CSHL Cold Spring Harbor Laboratory, USA; EBI European Bioinformatics Institute; EMBL European Molecular Biology Laboratory; HSPH Harvard School of Public Health, USA; LMB Laboratory of Molecular Biology, UK; MGH Massachusetts General Hospital, USA; Sanger Wellcome Trust Sanger Institute, UK
  3. c BBSRC Biotechnology & Biological Sciences Research Council, UK; HHMI Howard Hughes Medical Institute, US; NA not applicable; NCBI National Center for Biotechnology Information, US; NHMRC The National Health & Medical Research Council, Australia; NIH National Institutes of Health, US; NSF National Science Foundation, US; USDA-ARS United States Department of Agriculture - Agriculture Research Service; Packard David & Lucile Packard Foundation
  4. d Most highly cited associated publications (at most five)
  5. e Total number of citations, obtained from Google Scholar on Feb. 22, 2019