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 | 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 | 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 | NA | [28] | 24,261 | |
 MAFFT | 2013 | Kyoto U. | Ministry of Education, Culture, Sports, and Technology of Japan | 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 | 11,375 | |
 MEGA | 1993 | Penn. State U., Arizona State U. | NIH, NSF, Burroughs-Wellcome | 119,268 | |
 Mr. Bayes | 2001 | U. Rochester, Uppsala U. | NSF | 52,742 | |
 Mesquite | 2001 | U. Arizona, U. British Columbia | Packard, NSF | [46] | 7,693 |
 PhyML | 2003 | CNRS, Montpellier | Montpellier Genopole, InterEPST Bioinformatics Program | 24,614 | |
 PHAST | 2004 | UC Santa Cruz, Cornell | NSF, Packard, NIH | 4,690 | |
 RAxML | 2004 | Technical U. Munich | Heidelberg Institute for Theoretical Studies | 27,550 | |
 HyPhy | 2005 | UC San Diego, NC State | NA | [60] | 2,159 |
 BEAST | 2007 | U. Auckland, U. Edinburgh | Wellcome Trust, Royal Society | 12,027 | |
 FastTree/FastTree2 | 2009 | Lawrence Berkeley Nat’l Lab, UC Berkeley | DOE, GTL Program | 5,308 | |
Gene prediction, motif finding, and RNA folding | |||||
 MEME | 1994 | UC San Diego | NIH, NSF | 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 | 4,781 | |
Visualization | |||||
 Jalview | 1996 | EBI, Sanger, Oxford | BBSRC | 5,895 | |
 TreeView | 1998 | Stanford | NIH | [77] | 17,796 |
 UCSC Genome Browser | 2000 | UC Santa Cruz | NIH, DOE, HHMI | 11,365 | |
 ENSEMBL Browser | 2000 | EBI, Sanger | Wellcome Trust, NIH, EMBL | 5,235 | |
 Cytoscape | 2003 | Inst. Systems Biology, Whitehead Inst., UC San Diego | Pfizer, NIH, NSF | 17,862 | |
 IGV | 2011 | Broad | NIH | [91] | 4,678 |
Statistical and population genomics | |||||
 STRUCTURE | 2000 | Oxford | NIH, Burroughs-Wellcome, BBRC | 30,948 | |
 PHASE/fastPHASE | 2001 | Oxford, U. Washington | Wellcome Trust, BBSRC, Engineering and Physical Sciences Research Council | 10,073 | |
 ms | 2002 | U. Chicago | NA | [97] | 2,119 |
 PolyPhen | 2002 | EMBL, Max Delbrück Center for Mol. Med., Engelhardt Inst. Mol. Biol. | NIH | 11,136 | |
 SIFT | 2003 | Fred Hutchinson Cancer Res. Ctr. | NIH | 7,024 | |
 EIGENSTRAT | 2006 | Harvard, Broad | Millenium Pharmaceuticals, Burroughs Wellcome | [103] | 6,812 |
 PLINK | 2007 | MGH, Broad, U. Hong Kong | NIH | 17,938 | |
 TASSEL | 2007 | USDA-ARS, Cornell | USDA-ARS, NSF | [106] | 2,609 |
 BEAGLE | 2007 | U. Auckland | University of Auckland Research Committee, NIH | 2,997 | |
 IMPUTE/IMPUTE2 | 2007 | Oxford | Wellcome Trust, NIH | 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 | 5,965 | |
 TopHat/Cufflinks | 2009 | U. Maryland | NIH, NSF | 28,242 | |
 ChromHMM | 2010 | MIT, Broad | NSF, NIH | 3,977 | |
 BEDtools | 2010 | U. Virginia | NIH, Burroughs-Wellcome | 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 | 16,355 | |
Assembly, read mapping, and base/variant calling | |||||
 Staden package | 1977 | LMB | NA | 5,029 | |
 Phred | 1993 | Washington U., St. Louis, U. Washington | NIH | 12,172 | |
 MAQ | 2008 | Sanger | Wellcome Trust | [137] | 2,777 |
 ALLPATHS/ALLPATHS-LG | 2008 | Broad, MGH | NIH | 2,079 | |
 Velvet | 2008 | EBI | EMBL | [140] | 7,635 |
 Bowtie/Bowtie2 | 2009 | U. Maryland | NIH | 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 | 4,295 | |
 STAR | 2013 | CSHL | NIH | 6,013 |