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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