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Category Software Year
ToolKits and APIs Triplet-SVM 2005
Workflows OMIGA 2014
ToolKits and APIs Piano 2015
ToolKits and APIs LR50 2015
Aligners (short read) SMALT2010
Aligners (short read) MAQ2007
Assemblers Genomic (long read) MERACULOUS2010
Assemblers Genomic (short read) PE-ASSEMBLER2010
Genome Browsers NCBI MapViewer2004
Multiple Sequence Aligners PROBCONS2005
Multiple Sequence Aligners MAFFT2002
Sequence Tools Strelka2012
Sequence Tools CD-HIT2006
Structure Modelling PSIPRED1999
Structure Visualisation Jmol2001
ToolKits and APIs AMPLICONNOISE2010
ToolKits and APIs PLINK2007
ToolKits and APIs UTGB2007
ToolKits and APIs LAGAN2003
Workflows TAVERNA2003
Workflows eHIVE2000
Aligners (pairwise)JALIGNER2010
Aligners (pairwise)ZOOM2008
Aligners (pairwise)EXONERATE2005
Aligners (pairwise)ACT2005
Aligners (pairwise)SSAHA2003
Aligners (pairwise)BLAT2002
Aligners (pairwise)SSAHA22001
Aligners (pairwise)VMATCH2000
Aligners (pairwise)MASKERAID2000
Aligners (pairwise)MUMmer1999
Aligners (pairwise) HMMER1998
Aligners (pairwise)CROSSMATCH1992
Aligners (pairwise)BLAST NCBI1990
Aligners (pairwise)FASTA1988
Aligners (short read)CASAVAXX
Aligners (short read)rna-star2012
Aligners (short read)GMAP/GSNAP2011
Aligners (short read)BWA2009
Aligners (short read)BFAST2009
Aligners (short read)NOVOALIGN2009
Aligners (short read)SOAP2008
Aligners (short read)Bowtie2008
Assemblers (mRNA)Trinity2011
Assemblers (mRNA)OASES2010
Assemblers (mRNA)CUFFLINKS2009
Assemblers (mRNA)UNIGENE2003
Assemblers Genomic (long read)PRICE2011
Assemblers Genomic (long read)QUAKE2010
Assemblers Genomic (long read)FORGE2009
Assemblers Genomic (long read)OLIGOZIP2007
Assemblers Genomic (long read)NEWBLER2005
Assemblers Genomic (long read)SEQCLEAN2004
Assemblers Genomic (long read)PHUSION(2)2003
Assemblers Genomic (long read)ARACHNE2002
Assemblers Genomic (long read)PCAP2001
Assemblers Genomic (long read)MIRA 971997
Assemblers Genomic (long read)CELERA1997
Assemblers Genomic (short read)SPADES2012
Assemblers Genomic (short read)SOAP: DE NOVO 22009
Assemblers Genomic (short read)SGA2009
Assemblers Genomic (short read)BAMBUS 2 092009
Assemblers Genomic (short read)CONTRAIL2009
Assemblers Genomic (short read)ABYSS2009
Assemblers Genomic (short read)CORTEX_CON_RP2008
Assemblers Genomic (short read)ALLPATHS-LG2007
Assemblers Genomic (short read)VELVET2007
Database/WarehouseMISO2012
Database/WarehouseENA2012
Database/WarehousePFAM2011
Database/WarehouseCHADO2010
Database/WarehouseCHEBI2010
Database/WarehouseTRANSMART2009
Database/WarehouseCHEMBL2008
Database/WarehouseINTERMINE2007
Database/WarehouseBIOWAREHOUSE2006
Database/WarehouseINTERPRO2005
Database/WarehousebioMART2003
Database/WarehouseUNIPROT2003
Database/WarehousebioSQL2001
Database/WarehouseCATH1997
Database/WarehousePROSITE1989
Database/WarehouseGENBANK1982
Database/WarehousePDB1971
Gene Prediction (mRNA)SNAP2011
Gene Prediction (mRNA)MAKER2011
Gene Prediction (mRNA)AUGUSTUS2009
Gene Prediction (mRNA)MGENE2008
Gene Prediction (mRNA)JIGSAW2005
Gene Prediction (mRNA)ENSEMBL PIPELINE 2000
Gene Prediction (mRNA)EUGENE1999
Gene Prediction (mRNA)FGENESH1999
Gene Prediction (mRNA)GLIMMER 31998
Gene Prediction (mRNA)GENSCAN1997
Gene Prediction (ncRNA)RNAfold2010
Gene Prediction (ncRNA)MIRDEEP2008
Gene Prediction (ncRNA)tRNAscan1997
Genome BrowsersTRIPODXX
Genome BrowsersDALLIANCE BROWSER2010
Genome BrowsersSAVANT2010
Genome BrowsersIGV2008
Genome BrowsersARGO2007
Genome BrowsersJBROWSE2007
Genome BrowsersSEQMONK2007
Genome BrowsersIGB2004
Genome BrowsersAPOLLO2002
Genome BrowsersGBROWSE2002
Genome BrowsersARTEMIS2002
Genome BrowsersUCSC2001
Genome BrowsersENSEMBL BROWSER2000
Multiple Sequence AlignersPROT PAL2012
Multiple Sequence AlignersPRANK2010
Multiple Sequence AlignersFSA2008
Multiple Sequence AlignersPECAN2006
Multiple Sequence AlignersMAVID2004
Multiple Sequence AlignersMUSCLE2004
Multiple Sequence Aligners T-COFFEE2000
Multiple Sequence AlignersCLUSTALW1994
Other AlignersBismark2010
Other AlignersMauve2010
Other AlignersDALI2003
Sequence ToolsMUTECT2013
Sequence ToolsRSEM2012
Sequence ToolsFLEXBAR2012
Sequence ToolsVARIANTTOOLS2011
Sequence ToolsRNNOTATOR2011
Sequence ToolsANNOVAR2011
Sequence ToolsFastQC2010
Sequence ToolsDENDROPY2010
Sequence ToolsGENEPOOL2010
Sequence ToolsFASTX-Toolkit2009
Sequence ToolsMETABIOME2009
Sequence ToolsTOPHAT2008
Sequence ToolsGENEDATA2008
Sequence ToolsNESTEDMICA2005
Sequence ToolsJALVIEW2004
Sequence ToolsMEME2003
Sequence ToolsINTEGROMICS2003
Sequence ToolsMATCH2003
Sequence ToolsMASCOT1999
Sequence ToolsSRS1997
Sequence ToolsREPEATMASKER1996
Structure ModellingTARGETP2007
Structure ModellingHhpred2005
Structure ModellingSWISS-MODEL2003
Structure ModellingMODELLER2003
Structure ModellingTMHMM1998
Structure ModellingSIGNALP1997
Structure ModellingROSETTA1996
Structure ModellingTHREADER1992
Structure VisualisationPYMOLXX
Structure VisualisationCHIMERA2004
Structure VisualisationRasMol1995
ToolKits and APIsMRBAYESXX
ToolKits and APIsPARTEKXX
ToolKits and APIsGENESPRINGXX
ToolKits and APIsGENABEL2012
ToolKits and APIsSRNA WORKBENCH UEA2011
ToolKits and APIsAVADIS NGS2010
ToolKits and APIsSAMtools2009
ToolKits and APIsQIIME2009
ToolKits and APIsPicard2009
ToolKits and APIsVCFtools2009
ToolKits and APIsGATK2009
ToolKits and APIsDNANEXUS2009
ToolKits and APIsUGENE2008
ToolKits and APIsPATHWAY TOOLS2008
ToolKits and APIsAPSAMPLER2005
ToolKits and APIsGENEIOUS2005
ToolKits and APIsCLC BIO2005
ToolKits and APIsPHASTCONS2004
ToolKits and APIsBioPython2003
ToolKits and APIsBIOCONDUCTOR2001
ToolKits and APIs EMBOSS2000
ToolKits and APIs BIOJAVA2000
ToolKits and APIsENSEMBL API2000
ToolKits and APIsbioRUBY2000
ToolKits and APIsbioPERL2000
ToolKits and APIsPAML1997
ToolKits and APIsPHYLIP1981
WorkflowsGENEXPLAIN2010
WorkflowsKNIME2008
WorkflowsGALAXY2007
WorkflowsPIPELINE PILOT1999