name,Publication_id
"Mascot Server",10612281
microManager,20890901
PolyPhen-2,23315928
bedtools_genomecoveragebed_histogram,25199790
motif-x,21901740
FBAT,11055368
DSSP,6667333
AUGUSTUS,27322403
SPICE,21265010
FlowSOM,25573116
SWISS-MODEL,9504803
MACH,21058334
MaCH-Admix,23074066
"SNPs GO",19514061
"Collagen Mutation Database (CMD)",21520333
dbNSFP,21520341
"Cafe Variome",11295823
Orphadata,22422702
dbNSFP,23843252
Oncotator,25703262
GeneMatcher,26220891
PhenomeCentral,26251998
"Matchmaker exchange",26295439
dbNSFP,26555599
SPICKER,15011258
Chimera,15264254
AMBER,16200636
AutoDock,19399780
"AutoDock Vina",19499576
MDAnalysis,21500218
SwissParam,21541964
MassBank,20623627
NetPhosK,15174133
Libra,20101611
SearchGUI,21337703
Comet,23148064
FunRich,25921073
ModPred,24888500
"Clustal Omega",28884485
PHDhtm,7795533
CASTp,9761470
MolProbity,12557186
GOLD,12910460
TM-score,15476259
"CcpNmr Analysis",15815974
MUpro,16372356
ABCpred,16894596
ClusPro,16933295
PSVS,17186527
SCRWL,19603484
ClusPro,20818657
ProSA-web,8108378
"PEAKS De Novo",14558135
DEPIB,19415765
IBDfinder,9405095
reprof,8345525
SCOP,7723011
JEvTrace,8609628
GENSCAN,9149143
oligo-analysis,9719638
"Institute of Enzymology Servers",9769220
PSIPRED,10493868
NetPhos,10600390
3D-pssm,10860755
TargetP,10891285
T-Coffee,10964570
TMHMM,11152613
FUGUE,11419950
prof_sim,11827492
"MRC Image Processing Package",8742717
IMOD,8742726
SPIDER,8742743
LZerD,24573470
breseq_bam2cov,24838886
PRANK,24170401
AQUA,9008363
ChemProps,337120
Ginkgo,63440
"Reciprocal Smallest Distance (RSD)",593400
MISA,12589540
SMOOTH,16258753
NetChop,15744535
NetMHCpan,19002680
SYFPEITHI,10602881
OGdraw,17957369
GEC,22143225
HGMD,24077912
AllerTOP,24878803
ASNR,36810
GAP,46819
MichelaNglo,61125
"needle (EBI)",5420325
MetaSel,4564477
"Coriander Genomics Database",57241
"water_api (EBI)",7265238
Hydrophobicity,7108955
CPHmodels,20542
BENTO,23604
FASTA,2156132
PDR,61066
Ktreedist,890735
BAMscale,23215
flowClean,699050
PespotDB,3545499
NL4DV,3048704
ContigExtender,3370672
AREM,2203533
NJplot,8905155
PhenoModifier,164246
pksensi,334262
"Clustal 1.8 (Clustal W, Clustal X)",3243435
Dotter,8566757
"NDB Tools",1384741
RNAz,12079347
BLAST,2231712
"Andrej Sali Lab",14696385
oGNM,9218955
"Johns Hopkins Coronavirus Resource Center",32087114
Kaks_Calculator,20451164
iAMP-2L,23395824
iHSP-PseRAAAC,23756733
PseKNC,24732113
iTIS-PseTNC,25016190
iDNA-Methyl,25596338
iRNA-Methyl,26314792
iSuc-PseOpt,26723495
pRNAm-PC,26748145
GCTA,21167468
Condel,21457909
SCORE-Seq,21885029
xhmm,23040492
SKAT,23684009
MetaSKAT,23768515
RFMix,23910464
InterVar,28132688
ClinPred,30220433
MSMBuilder,28076801
Intogen,25759023
smirnaDB,17604727
NetworKIN,17570479
PROTOMAP,18724940
mEAT,20371350
CompositeDriver,29625053
SeneQuest,31675495
Trinotate,28099853
Juicebox,27467249
r-bseqsc,27667365
MHCflurry,29960884
CoroNet,32534344
AtbPpred,31372196
EpiEstim,31624039
"AceView genes database",20064451
REDCap,18929686
"SILVA rRNA database",28648396
Phobius,15111065
"Institute of Enzymology Servers",15769473
PDBePISA,17681537
HADDOCK,26410586
BlastKOALA,26585406
"MMTSB toolset",15099834
SerialEM,16182563
Frealign,16828314
EMAN,16859925
XMIPP,24075951
"SCIPION WEB TOOLS",27108186
iHyd-PseAAC,21168420
iCDI-PseFpt,23988798
iPPI-Esml,25908206
pSuc-Lys,26807806
TBtools,32585190
UALCAN,28732212
LST,22119648
SOLAR-eclipse,25747917
Lead-DBS,30179717
MRtrix3,31473352
Meta-4mCpred,31146255
SDM6A,31542696
DisEMBL,14604535
MonoRes,29395788
TubercuList,20980199
iDNA6mA-PseKNC,29360500
MITOS,22982435
GS-align,25819445
PASS,92183
"Clustal W",8743695
Raster3D,18488322
QuEST,60518
"The Allele Frequency Net Database (AFND)",72239
SAAP-BS,89387
EMBOSS,10827456
VAST,8804824
RasMol,7482707
"Clustal 2 (Clustal W, Clustal X)",9810230
PSORT.org,10087920
Swiss-PdbViewer,10470037
QMol,11552684
srnaloop,12769849
"NDB Tools",11345429
VEGAS2,25518859
PeptideProphet,12403597
ProteinProphet,14632076
ASAPRatio,14640741
PepNovo,15858974
InsPecT,16013882
mzMatch,21401061
CAMERA,22111785
r-recetox-xmsannotator,27977166
CHARMM-GUI,30525595
PEP-FOLD,26588162
HADDOCK,12580598
OMSSA,15473683
MyriMatch,17269722
Panorama,25102069
PsRRR,2982105
MSCquartets,3031510
ePMV,2139718
AppleMDO,1695717
"Pseudomonas Genome Database",10984043
Cox-PASNet,1865908
Quant,1758493
"Rat Genome Database (RGD)",1560824
Ampred,11807545
"GO enrichment analysis tool",10802651
Scansite,11283593
PharmGKB,22992668
NetOGlyc,23584533
"PhenX Toolkit",26938784
tax2tree,22134646
expressbetadiversity,22402401
dRep,28742071
vcf2diploid,21811232
"Clustal Omega",21988835
ActiveDriver,22395476
ActiveDriver,23340843
"Visualisation tools",16729048
Phusion,12466850
"Yeast GFP fusion localization database (yeastgfp)",14562095
"International HapMap Project",14685227
"Allen Brain Atlas-API",17151600
SNPTEST,17554300
"International HapMap Project",17943131
"International HapMap Project",17943122
"DeltaG prediction",18075582
"SGRP Blast Server",19212322
Phusion,19606140
Phusion,19606141
SeqMonk,20098412
Enterotyping,21508958
PSMC,21753753
BrainCloud,22031444
"Banana Genome Hub",22801500
MutSig2CV,23770567
MutSig2CV,24390350
DNENRICH,24463507
ProteomicsDB,24870543
"ROADMAP epigenomics",25693563
methylpy,26030523
abawaca,26083755
1000Genomes,26432245
SalmoBase,27088604
gnomAD,27535533
"BioPlex 2.0",28514442
CASSys,18978777
SPP,19029915
MaxQuant,19029910
PeakSeq,19122651
Cufflinks,20436464
GREAT,20436461
Scripture,20436462
IGV,21221095
Trinity,21572440
mutmap,22267009
ProteoWizard,23051804
Cufflinks,23222703
MuTect,23396013
PICRUSt,23975157
LACHESIS,24185095
ProteomeXchange,24727771
OpenSWATH,24727770
Sailfish,24752080
mgs-canopy,24997787
scLVM,25599176
Peptide-shaker,25574629
StringTie,25690850
ballgown,25748911
COMPASS,26006008
kallisto,27043002
GNPS,27504778
EVmutation,28092658
GuideScan,28263296
Nextflow,28398311
demuxlet,29227470
FORECasT,30480667
XPRESS,11581660
Tango,15361882
AlignACE,9788350
ENDEAVOUR,16680138
APEX,17187058
MiRDeep,18392026
Batman,18612301
MDscan,12101404
RODEO,28244986
Kaiju,27071849
MS-GF+,25358478
Cortex,18311140
Cortex,22231483
"ISA tools",18327258
GEMMA,22706312
GTEx,23715323
CADD,24487276
MSMC,19151714
MSMC,24952747
platypus,19098910
platypus,25017105
DISCOVAR,19377478
bolt-lmm,25642633
"Genome STRiP",19252488
LDSC,25642630
DANPOS,26301496
RTNduals,19270705
viper,27322546
Minimac3,19377477
Minimac3,27571263
CESAM,27869826
Graphtyper,19525955
MrCaNaVaR,19718026
EMMAX,20208533
Syzygy,20818383
"Cocoa Genome Hub",21186351
gatk2_haplotype_caller-IP,21478889
ELAND,18204446
ELAND,21499247
"Brassica Genome",18264096
"Brassica Genome",21873998
GenMAPP,11984561
GenePattern,16642009
"dbEST database of EST sequences",8401577
silcLOD,7581446
PicTar,15806104
hgv_beam,17721534
FLOSS,11731797
deCODE,12053178
"Mosaic Vaccine Designer",17187074
ERANGE,18516045
QuEST,19160518
SegSeq,19043412
Phymm,19648916
PyroNoise,19668203
BreakDancer,19668202
r-cssam,20208531
ALEXA-Seq,20835245
Trans-ABySS,20935650
MISO,21057496
SAINT,21131968
FaST-LMM,21892150
SignalP,21959131
SHAPEIT,22138821
HH-suite,22198341
ChromHMM,22373907
"Bowtie 2",22388286
IMEx,22453911
Segway,22426492
clusterone,22426491
FaST-LMM,22669648
MetaPhlAn,22688413
"ImageJ (NIH)",22930834
"GEM-Mapper v3",23103880
express-IP,23160280
SpecI,23892899
Intogen,24037244
metagenomeSeq,24076764
"Metagenomic operational taxonomic units (mOTUs)",24141494
E-CRISP,24481216
pyclone,24633410
MutationTaster,24681721
scde,24836921
concoct,25218180
RnBeads,25262207
Diamond,25402007
ABarray,25633503
DIA-Umpire,25599550
HISAT2,25751142
CIBERSORT,25822800
MiXCR,25924071
SVTyper,26258291
Oscope,26301841
RiboTaper,26657557
dada2,27214047
IHW,27240256
TRIC,27479329
CRAC,27941783
monocle,28114287
cryoSPARC,28165473
nanopolish,28218898
signalAlign,28218897
MotionCor2,28250466
Salmon,28263959
umis,28263961
SC3,28346451
SCnorm,28418000
CIRCLE-seq,28459458
sleuth,28581496
histoCAT,28783155
chromVAR,28825706
"Monocle 2",28825705
MECAT,28945707
AUCell,28991892
scmap,29608555
QIIME,20383131
POLYPHEN,20354512
SHOREmap,19644454
MutationTaster,20676075
drFAST,20676076
iceLogo,17934469
Percolator,17952086
matchBox,15846361
decoy.pl,16118637
CNSsolve,18007608
hgv_david,19131956
RTAnalyzer,18546601
biomaRt,19373228
biomaRt,19617889
HADDOCK,20431534
"Differential RNA-seq pipeline",22383036
"Post Assembly Genome Improvement Toolkit",22678431
RaptorX,22814390
modencode_peakcalling_macs2-IP,22936215
EasyQC,24762786
NetworkAnalyst,25950236
Phyre,25950237
HISAT2,27560171
primalscheme,28538739
SNPTEST,20517342
CoNet,22796884
"The Protein Data Bank (PDB)",14634627
SymCurv,19684599
nanosv,29109544
zinbwave,29348443
MetaNeighbor,29491377
r-scimpute,29520097
"Sugarcane Genome Hub",29980662
DCA,30674886
Metascape,30944313
TYGS,31097708
Enterotyping,29255284
das_tool,29807988
velocyto.py,30089906
inDelphi,30405244
magpurify,30867587
HMP2,31142855
Flye,30936562
scanorama,31061482
hisat2,31375807
QIIME2.0,31341288
PICRUSt2,32483366
BiG-SCAPE,31768033
NGMLR,29713083
Bioconda,29967506
HUMAnN2,30377376
scScope,30886411
Py-EM,31086343
Prosit,31133760
Garnett,31501545
Warp,31591575
ilastik,31570887
Harmony-R,31740819
wtdbg2,31819265
"COBRA Toolbox",30787451
MicrobiomeAnalyst,31942082
PhageTerm,28811656
CMScaller,29192179
QuPath,29203879
encode-blacklist,31249361
HydDB,27670643
SwissADME,28256516
iLoc-Cell,22134333
ReactomePA,26661513
IGPred,26883492
TCS,11050560
Gene-PROBER,335245
NERDD,77475
OpenCASA,306577
ParDRe,6803159
multiplierz,1987460
pymbar,19045004
"PRANK API",16000407
RNAz,15665081
GSEA,16199517
MotifRegressor,12626739
JSpecies,19855009
ASCAT,20837533
Allpaths-LG,21187386
pmdtools,24469802
2020plus,27911828
"Mammalian Gene Collection",12477932
consensusDE,184458
WheatQTLdb,341152
NetGSA,341157
BioNetFit,265563
DeepRKE,333431
gprege,215999
CScape-somatic,228288
"La isla de tomato",316537
Luciphor2,42906
CemrgApp,41243
CEQer,41244
LINKAGE,6587361
PHI-Nets,3186695
FASTA,3162770
PepServe,2157210
Multi-Harmony,2052578
"Reciprocal Best Hits - Best Bidirectional Hits",10077608
RosettaDesign,10984534
"PEAKS DB",22186715
Mayu,19608599
iDrug-Target,25513722
SSAMK,12116640
PhyML,14530136
PhyML,16785212
GeneSplicer,11222
INFO-RNA,167095
DATMA,53263
Pedcheck,9634505
QTDT,10631157
PHASE,14574645
infocalc,14631557
"LD Select",14681826
SNPSpD,14997420
ADMIXMAP,15088268
ANCESTRYMAP,15088269
fastPHASE,16532393
SABER,16773560
GMDR,17503330
PLINK,17701901
BEAGLE,17924348
RADIOMICS,26119045
GINsim,11911796
Ray,20958248
HotNet,21385051
Opera,21929371
IsoLasso,21951053
SPAdes,22506599
clusterProfiler,22455463
r-sequenza,25319062
RAM-ESVM,31609411
MEGA,15260895
"MAFFT (REST)",18372315
"Pathway Tools",19955237
IGVtools,22517427
MAFFT,28968734
ANPELA,30649171
TREECON,7828077
TreeView,8902363
PAML,9367129
SOSUI,9632836
ModelTest,9918953
"ESPript 3.0",10320398
SPACE,10320401
VISTA,11159318
PSIPRED,10869041
DaliLite,10980157
Lucy,11751217
MotifSampler,11751219
MEGA,11751241
KNNimpute,11395428
MrBayes,11524383
HMMTOP,11590105
Twinscan,11473003
PSORT.org,11847077
ALGGEN,11847087
ms,11847089
TREE-PUZZLE,11934758
vsn,12169536
RMAExpress,12538238
"Clustal 1.8 (Clustal W, Clustal X)",1591615
SBML,12611808
AUGUSTUS,14534192
R-QTL,12724300
3D-Jury,12761065
ClusPro,14693807
affycomp,14960458
FatiGOplus,14990455
XTandem,14976030
Glimmer-HMM,15145805
"Java Treeview",15180930
RNSC,15180928
Randfold,15217813
CAPweb,15381628
"Generic GO Term Finder",15297299
HaploView,15297300
PILER,15961452
SGA,16204131
HH-suite,15531603
safe,15647293
ProtTest,15647292
GMAP,15728110
KOBAS,15817693
PMut,15879453
biomaRt,16082012
RONN,15947016
"Institute of Enzymology Servers",15955779
BiNGO,15972284
simpleaffy,16076888
Blast2GO,16081474
aCGH,16159913
RLMM,16267090
SWISS-MODEL,16301204
Paircoil2,16317077
affylmGUI,16455752
topGO,16606683
RankProd,16982708
COPASI,17032683
"Interactive Tree Of Life (iTOL)",17050570
GOstats,17098774
ARIA,17121777
SSAKE,17158514
Glimmer,17237039
Gepard,17309896
CEGMA,17332020
GEOquery,17496320
"VIPER LC-MS",17545182
TASSEL,17586829
beadarray,17586828
"Clustal 2 (Clustal W, Clustal X)",17846036
VCAKE,17893086
AUGUSTUS,18218656
SOAP,18227114
LibSBML,18252737
DAnTE,18453552
Ontologizer,18511468
"FindPeaks 4.0 (Vancouver Short Read Package)",18599518
mzR,18606607
ZOOM,18684737
SeqMap,18697769
ADZE,18779233
F-seq,18784119
CABOG,18952627
SPIA,18990722
DNAPlotter,18990721
CleaveLand4,19017659
"AmiGO 2",19033274
arrayQuality,19106121
"IslandViewer 4",19151094
Jalview,19151095
QMSIM,19176551
INTEGRALL,19228805
TopHat,19289445
Biopython,19304878
CloudBurst,19357099
BWA,19451168
rtracklayer,19468054
SOAP,19497933
SICER,19505939
trimAl,19505945
BCF-Tools-Cat-IP,19505943
VarScan,19542151
Pindel,19561018
"SNP ratio test",19620097
IGB,19654113
MutPred,19734154
QuickGO,19744993
DEGseq,19855105
Tablet,19965881
RSEM,20022975
BWA,20080505
BEDTools,20110278
SNVMix,20130035
Skyline,20147306
GSNAP,20147302
GOSemSim,20179076
Bubastis,20200009
PheWAS,20335276
ConsensusClusterPlus,20427518
DendroPy,20421198
TAPIR,20430753
PSORTb,20472543
fastq_groomer_parallel,20562416
Metal,20616382
bedGraphToBigWig,20639541
"Cytoscape Web",20656902
oligo,20688976
GeneMANIA,20926419
SSPACE,21149342
AUGUSTUS,21216780
Jellyfish,21217122
PRINSEQ,21278185
BeatsonLab-MicrobialGenomics,21278367
meme_fimo,21330290
Bismark,21493656
ProDy,21471012
BamTools,21493652
SequenceVariantAnalyzer,21624899
VCFtools,21653522
Cufflinks,21697122
RUM,21775302
ContEst,21803805
ExomeCNV,21828086
ChimeraScan,21840877
Seal,21856737
FLASH,21903629
Pybedtools,21949271
PoPoolation2,22025480
pgdspider,22110245
Control-FREEC,22155870
ESpritz,22190692
Artemis,22199388
ART,22199392
"Multi Experiment Matrix",22247279
Oases,22368243
Rehh,22402612
Contra,22474122
GEM,22492648
RNA-SeQC,22539670
Geneious,22543367
"SILVA rRNA database",22556368
BitSeq,22563066
Strelka,22581179
Bedops,22576172
"ADAPTER REMOVAL",22628521
GUniFrac,22711789
RSeQC,22743226
Delly2,22962449
GAPIT,22796960
Snakemake,22908215
QualiMap,22914218
CD-HIT-IP,23060610
HiCNorm,23023982
Vmatch,23060614
SNPRelate,23060615
SortMeRna,23071270
STAR,23104886
Bedutils,23314324
RepeatExplorer,23376349
QUAST,23422339
EBSeq,23428641
TANGO,23681123
pathview,23740750
KmerGenie,23732276
OncodriveCLUST,23884480
NextGenMap,23975764
MaSuRCA,23990416
PEAR,24142950
AllergenFP,24167156
MEDIPS,24227674
FeatureCounts,24227677
NextClip,24297520
CrossMap,24351709
MSIsensor,24371154
"InterProScan (EBI)",24451626
RAxML,24451623
ngsTools,24458950
bumphunter,24478339
iNuc-PseKNC,24504871
PyRAD,24603985
pRESTO,24618469
Prokka,24642063
trimmomatic,24695404
ThunderSTORM,24771516
MSstats,24794931
SAMBLASTER,24812344
MIPgen,24867941
proovread,25015988
circlize,24930139
STAMP,25061070
SVDquartets,25104814
LoRDEC,25165095
Poretools,25143291
HTSeq,25260700
A5-miseq,25338718
DOSE,25677125
"minimac 2",25338720
"UniProt Reference Clusters (UniRef)",25398609
CRISPRdirect,25414360
MetaPSICOV,25431331
GSDS,25504850
NMRFAM-SPARKY,25505092
PRSice,25550326
MethylMix,25609794
MEGAHIT,25609793
PolyMarker,25649618
SNN-Cliq,25805722
Sambamba,25697820
vt,25701572
ChIPseeker,25765347
MeDuSa,25810435
HAlign,25812743
ExaML,25819675
ASTRAL,26072508
AncesTree,26072510
polyester,25926345
Tax4Fun,25957349
GOplot,25964631
Mango,26034063
BUSCO,26059717
Bandage,26099265
USEARCH,26139637
LDlink,26139635
SomaticSignatures,26163694
Roary,26198102
missMethyl,26424855
LOLA,26508757
tcsBU,26515821
MaxBin,26515820
PHYLUCE,26530724
BRAKER1,26559507
genefu,26607490
MetaQUAST,26614127
Manta,26647377
destiny,26668002
ComplexHeatmap,27207943
MultiQC,27312411
Assemblytics,27318204
pSumo-CD,27354696
MorphoLibJ,27412086
PRODIGY,27503228
Cas-analyzer,27559154
KAT,27797770
minfi,28035024
scater,28088763
mPTP,28108445
synergyfinder,28379339
"Trainable Weka Segmentation",28369169
"Crop Analysis Tool Suite (CATS)",28398459
karyoploteR,28575171
UpSetR,28645171
DeepLoc,29036616
VICTOR,29036289
iDNA4mC,28961687
mosdepth,29096012
DFAST,29106469
FROGS,29228191
MAFFT,29506019
NanoPack,29547981
Minimap2,29750242
IRscope,29659705
iTerm-PseKNC,30247625
PopLDdecay,30321304
RAxML-NG,31070718
GTDB-Tk,31730192
KofamKOALA,31742321
RMAExpress,12925520
TCC,17728317
"Conditional quantile normalization",22285995
"ICGC Data Portal",21930502
PhenoDigm,23660285
DisGeNET,25877637
MetaGeneAnnotator,18940874
SOAPnuke,29220494
MendelianRandomization,28398548
ResFinder,22782487
PAML,17483113
MEGA,17488738
FastTree,19377059
SeaView,19854763
MEGA,21546353
BEAST,22367748
LFMM,23543094
r-popgenome,24739305
selscan,25015648
iqtree,25371430
FastME,26130081
PhyML+SMS,28472384
UFBoot2,29077904
DAMBE7,29669107
SLiM,30517680
ModelTest-NG,31432070
SVAMP,2470031
MIRIA,1861975
ClustalW,7984417
PolyPhred,9207020
"PSI-BLAST (EBI)",9254694
"Clustal 1.8 (Clustal W, Clustal X)",9396791
"Saccharomyces genome database (SGD)",9399804
"Kyoto encyclopedia of genes and genomes (KEGG)",9847135
TRF,9862982
"NCBI Taxonomy Database",10592170
"The Protein Data Bank (PDB)",10592235
"ProDom protein domain database",10592243
"ENZYME - Enzyme nomenclature database",10592255
COGs,11125040
SNPdb,11125122
"R functions for cDNA array analysis",11410663
REPuter,11713313
GeneSplicer,11222768
"NCBI GEO",11752295
SCOP,11752311
"Database of interacting proteins (DIP)",11752321
Ensembl,11752248
genomation,25417
mafft,12136088
"Ribosomal Database Project (RDP)",12520046
"BIND SOAP",12519993
Entrez,12519940
"Stanford Microarray Database (SMD)",12519956
Ensembl,12519943
CD-Search,12520028
MIAMExpress,12519949
TRANSFAC,12520026
"PANTHER Tools",12520017
"UCSC C. briggsae Genome Browser Gateway",12519945
ClustalW,12824352
hgv_sift,12824425
GlobPlot,12824398
SWISS-MODEL,12824332
ELMInstanceMapper,12824381
"ENDscript 2.0",12824317
ExPASy,12824418
AS2TS,12824330
Scansite,12824383
Match,12824369
Mfold,12824337
"Vienna RNA Package",12824340
ALGGEN,12824386
ESEfinder,12824367
SWISS-MODEL,14681401
JASPAR,14681366
CSS,14681376
"Saccharomyces genome database (SGD)",14681421
Ensembl,14681459
SCOP,14681400
"Database of interacting proteins (DIP)",14681454
siDirect,14769950
ARB,14985472
"Berkeley Phylogenomics Group",15034147
ClusPro,15215358
DICHROWEB,15215473
PredictProtein,15215403
AUGUSTUS,15215400
PDB2PQR,15215472
MolProbity,15215462
FATCAT,15215455
CD-Search,15215404
VISTA,15215394
"Web Weeder",15215380
Robetta,15215442
"Stanford Microarray Database (SMD)",15608265
"NCBI Taxonomy Database",15608257
OMIM,15608251
"PANTHER Tools",15608197
Inparanoid,15608241
Ensembl,15608235
PhyML,15980534
MicroInspector,15980566
snoGPS,15980563
I-MUTANT,15980478
JCat,15980527
miRU,15980567
FoldX,15980494
OrfPredictor,15980561
SCRATCH,15980571
HHpred,15980461
"UCL Servers",15980489
ProFunc,15980588
FFAS,15980471
AUGUSTUS,15980513
H++,15980491
WebGestalt,15980575
PatchDock,15980490
tmalign,15849316
BASys,15980511
NRPSpredictor2,16221976
DrugBank,16381955
"The GRID",16381927
Ensembl,16381931
TRANSFAC,16381825
"PubMed Central",16381840
WEGO,16845012
"PROSITE Scan (EBI)",16845026
KOBAS,16845106
CUPSAT,16845001
"MEME Suite",16845028
AUGUSTUS,16845043
FastSNP,16845089
NAST,16845035
"QGRS Mapper",16845096
CASTp,16844972
PAL2NAL,16845082
AlgPred,16844994
VISTA,17130149
"LIPID MAPS",17098933
"NCBI reference sequences",17130148
HMDB,17202168
Ensembl,17148474
"BindingDB database of measured binding affinities",17145705
QuantiSNP,17341461
RNAmmer,17452365
MolProbity,17452350
g:Profiler,17478515
"WoLF PSORT",17517783
STAMP,17478497
PDB2PQR,17488841
LTR_Finder,17485477
ProSA-web,17517781
Primer3Plus,17485472
KAAS,17526522
CRISPRFinder,17537822
PrDOS,17567614
CPC,17631615
"DAVID Bioinformatics Resources",17576678
PIC,17584791
"Complete Arabidopsis transcriptome database",17940091
PPS,17962309
"SILVA rRNA database",17947321
"IMG M",17932063
"Kyoto encyclopedia of genes and genomes (KEGG)",18077471
JASPAR,18006571
Ensembl,18000006
SCOP,18000004
CGView,18411202
Phylogeny.fr,18424797
FireDock,18424796
NetMHC-3.0,18463140
"Jpred 3",18463136
CS23D,18515350
"IMGT V-QUEST",18503082
SISSRs,18684996
"Pathway Interaction Database (PID)",18832364
"CiteXplore literature database",18940862
HMDB,18953024
"Plasmodium genome resources (PlasmoDB)",18957442
Ensembl,19033362
CEGMA,19042974
"The Immune Epitope Database (IEDB)",19906713
PrimerBank,19906719
"Gene Ontology (GO)",19920128
"Human Splicing Finder",19339519
SNPinfo,19417063
"DIANA-microT v5.0",19406924
"MEME Suite",19458158
"PREP Suite",19433507
MiRanalyzer,19433510
"MetaboAnalyst 2.0",19429898
GeneCodis3,19465387
"ToppGene Suite",19465376
Cadnano,19531737
BioPortal,19483092
"PubChem BioAssay Service",19498078
SoyBase,20008513
TransmiR,19786497
"Kinetoplastid genome resources (TritryPDB)",19843604
REBASE,19846593
MetaCyc,19850718
NNDB,19880381
RegPrecise,19884135
CORUM,19884131
MicrobesOnline,19906701
"UCSC Genome Browser",19906737
JASPAR,19906716
eggNOG,19900971
"ENCODE DCC",19920125
"NCBI Resources",19910364
Ensembl,19906699
Solas,20150413
CATH,21097779
Reactome,21067998
SRA,21062823
miRBase,21037258
"The RNA Modification Database (RNAMDB)",21071406
"Pathway Commons",21071392
ArrayExpress,21071405
starBase,21037263
RBPDB,21036867
Phospho.ELM,21062810
HSSP,21071423
miRTarBase,21071411
"The BioGRID Interaction Database",21071413
lncRNAdb,21112873
"PlantTFDB 2.0",21097470
EcoCyc,21097882
PHOSIDA,21081558
HIT,21097881
"NCBI Resources",21097890
"NCBI GEO",21097893
"Conserved domain database CDD",21109532
"Entrez Gene",21115458
RATT,21306991
seqMINER,21177645
QuasR,20371516
TranslatorX,20435676
agriGO,20435677
MIRU-VNTRplus,20457747
Dali,20457744
3DLigandSite,20513649
"UCL Servers",20507913
GUIDANCE,20497997
FoXS,20507903
SMOG,20525782
RegPredict,20542910
GeneMANIA,20576703
ANNOVAR,20601685
MapSplice,20802226
ShoRAH,20671025
FragGeneScan,20805240
"Sol Genomics Network",20935049
"PseudoCAP pseudomonas genome database",20929876
IKMC,20929875
TADB,20929871
COSMIC,20952405
CLIPZ,21087992
YEASTRACT,20972212
"UCSC Genome Browser",22075998
MetaCyc,22102576
"Gene Ontology (GO)",22102568
"Saccharomyces genome database (SGD)",22110037
FlyBase,22127867
"Database for Bacterial Group 2 Introns",22080509
"Integrated Microbial Genomes (IMG)",22194640
GABI-Kat,22080561
"UCSC Genome Browser",22086951
eggNOG,22096231
"NCBI reference sequences",22121212
"The Arabidopsis information resource (TAIR)",22140109
PhosphoSitePlus,22135298
PubChem,22140110
"TarBase v8",22135297
NONCODE,22135294
"NCBI Taxonomy Database",22139910
"NCBI Resources",22140104
"Interactive Tree Of Life (iTOL)",21470960
"T-Coffee (SIB)",21558174
R.E.D.,21609950
psRNATarget,21622958
NRPSpredictor2,21558170
SwissDock,21624888
HMMER3,21593126
g:Profiler,21646343
antiSMASH,21672958
PHAST,21672955
SNVer,21813454
"Orientations of Proteins in Membranes database",21890895
"ChEMBL API",21948594
ExoCarta,21989406
SRA,22009675
"Cone snail toxin database ConoServer",22058133
MINT,22096227
Phytozome,22110026
DO,22080554
MEROPS,22086950
VFDB,22067448
cn.mops,22302147
edgeR,22287627
PROSITE,23161676
QuaternaryProd,23203871
"GenBank nucleotide sequence database",23193287
"SILVA rRNA database",23193283
"TIGRFAMS  protein family database",23197656
DIANA-LNCBase,23193281
Segway,23221638
iRSpot-PseDNC,23303794
COFACTOR,22570420
"MetaboAnalyst 2.0",22553367
H++,22570416
ExPASy,22661580
GeneCodis3,22573175
PEP-FOLD,22581768
IEDB-AR,22610854
dbCAN,22645317
"DIANA miRPath",22649059
METAGENassist,22645318
SIFT,22689647
RobiNA,22684630
Primer3,22730293
TALE-NT,22693217
"The Flux Capacitor",22962361
MetaVelvet,22821567
OncodriveFM,22904074
SILVAngs,22933715
miRmap,23034802
HPO,24217912
GWIPS-viz,24185699
ClinVar,23444143
ClinVar,24234437
IntAct,24234451
UniProtKB,24253303
"IUPHAR BPS Guide to PHARMACOLOGY",24234439
"eFetch Pmc",24259429
"Carbohydrate-active enzymes database (CAZy)",24270786
"SILVA rRNA database",24293649
dbGAP,24297256
"GWAS catalog",24316577
"RDP Pyrosequencing Pipeline",24288368
Rsubread,23558742
"Apache Taverna",23640334
"EBI Tools",23671338
ComiR,23703208
PSIPRED,23748958
IgBLAST,23671333
aLeaves,23677614
BAGEL3,23677608
"DIANA-microT v5.0",23680784
WebGestalt,23703215
PubTator,23703206
antiSMASH,23737449
GalaxyRefine,23737448
GeneMANIA,23794635
JASPAR,24194598
STRING,25352553
Ensembl,25352552
iPro54-PseKNC,25361964
"DSSP secondary structure database",25352545
"Infernal cmscan",25392425
"Human gene nomenclature database (HGNC)",25361968
"IMGT HLA Sequence Alignment",25414341
"GO enrichment analysis tool",25428369
Gubbins,25414349
"Conserved domain database CDD",25414356
SwissTargetPrediction,24792161
"SWISS-MODEL Workspace",24782522
"CopraRNA web server",24838564
DeepTools,24799436
PASTA,24848016
CHOPCHOP,24861617
DUET,24829462
CFM-ID,24895432
"LINCS Canvas Browser (LCB)",24906883
LeeHom,25100869
"Simple modular architecture research tool (SMART)",25300481
MobiDB,25361972
"UniProt Align",25348405
limma,25605792
dbSUPER,26438538
WikiPathways,26481357
"Expression Atlas",26481351
SIDER,26481350
"MEROPS Blast",26527717
"Assembly converter",26687719
JASPAR,26531826
GPCRDB,26582914
"Ensembl Genomes",26578574
eggNOG,26582926
DIANA-LNCBase,26612864
"Reactome Small Molecule Search",26656494
TCGAbiolinks,26704973
PLIP,25873628
GUIDANCE2,25883146
I-TASSER,25883148
PHMMER,25943547
DIANA-mirPath,25977294
antiSMASH,25948579
Pse-in-One,25958395
ClustVis,25969447
TOPCONS,25969446
OrthoVenn,25964301
NOISeq,26184878
rgi,27789705
SRAMP,26896799
"ChEMBL BLAST Search",27899562
InterPro,27899635
OrthoDB,27899580
"SWISS-MODEL Repository",27899672
g:Profiler,27098042
vardict,27060149
HaploGrep,27084951
IQ-TREE,27084950
deeptools,27079975
"Interactive Tree Of Life (iTOL)",27095192
2bwt-builder-IP,27137889
"Bioinformatics Toolkit",27131380
PHASTER,27141966
Trnascan-SE,27174935
TSCAN,27179027
FACETS,27270079
REDIportal,27587585
stringApp,27924014
DisGeNET,27924018
novoplasty,28204566
ExAC,27899611
MarCat,28335016
Rfam,29112718
rWikiPathways,29136241
MobiDB,29136219
GPCRDB,29155946
JASPAR,29140473
"TarBase v8",29156006
GEPIA,28407145
TAREAN,28402514
"antiSMASH 4.0",28460038
"PRISM 3",28460067
PharmMapper,28472422
GeSeq,28486635
CPC2,28521017
NOREVA,28525573
RMBase,29040692
"BioGRID Open Repository of CRISPR Screens (ORCS)",30476227
eggNOG,30418610
DynaMut,29718330
"MetaboAnalyst 4.0",29762782
galaxy-util,29790989
BAGEL4,29788290
WEGO2.0,29788377
dbCAN2,29771380
CRISPCasFinder,29790974
"SWISS-MODEL Workspace",29788355
MiGA,29905870
BeStSel,29893907
GENCODE,30357393
DisGeNET,31680165
"Interactive Tree Of Life (iTOL)",30931475
AnnoTree,31081040
"EBI Search",30976793
NGphylogeny.fr,31028399
antismash,31032519
g:Profiler,31066453
"BioSeq-Analysis 2.0",31504851
miRDB,31504780
gutMDisorder,31584099
"MIBiG 2.0",31612915
miRNATarBase,31647101
"The Comprehensive Antibiotic Resistance Database (CARD)",31665441
TTD,31691823
RMAExpress,12582260
BIONJ,9254330
SGI,10563013
LIGPLOT,7630882
SecretomeP,15115854
PhyML,20525638
BEAGLE,21963610
Dendroscope3,22780991
tracer,29718447
FALC-Loop,1576220
"AGS ACN",8806
"FACTA plus",187721
OAT,26585518
Flye,31483244
RePAIR,3360322
SIMLD,2123466
WGAViewer,18256235
EDENA,18332092
"Ensembl Compara",19029536
Velvet,18349386
MAQ,18714091
Shore,18818371
MEDME,18765822
GERMLINE,18971310
GeneMark,18757608
SOAPsnp,19420381
VariationHunter,19447966
ABySS,19251739
Circos,19541911
RDXplorer,19657104
Admixture,19648217
JBrowse,19570905
SOAPdenovo,20019144
Geneid,10779490
PipMaker,10779500
GLASS,10899144
CNVer,20805290
GATK,20644199
Stampy,20980556
Dindel,20980555
ChimeraSlayer,21212162
QCALL,20980557
CNVnator,21324876
Dendrix,21653252
MEGAN6,21690186
Cytoscape,14597658
MuSiC2,22759861
LobSTR,22522390
phantompeakqualtools,22955991
ATARiS,23269662
FitHiC,24501021
"The Human Protein Reference Database (HPRD)",14525934
TitanCNA,25060187
GOTHiC,25752748
CheckM,25977477
Wise2.4,15123596
MIRA,15140833
nucleoatac,26314830
Multiz,15060014
HiRise,26848124
SSAHA,11591649
transrate,27252236
UMI-tools,28100584
Centrifuge,27852649
spades,28298430
Supernova,28381613
CANU,28298431
hicrep,28855260
Mauve,15231754
BLAT,11932250
ProbCons,15687296
"Yeast gene order browser",16169922
MAPP,15965030
SweeD,16251466
MEGAN,17255551
SHARCGS,17908823
PyroMap,17600086
MiRScan,17989254
MAKER,18025269
PennCNV,17921354
ALLPATHS,18340039
"PANTHER Tools",12952881
Phred,9521921
"Phred Phrap Consed Cross match",9521923
SIM4,9750195
WebLogo,15173120
SGP2,12529313
"CAP3 Sequence Assembly Program",10508846
LAGAN,12654723
"IMGT V-QUEST",21632778
expVIP,26869702
Phaser,19461840
Coot,15572765
PDBeFold,15572779
Auto-Rickshaw,15805600
buccaneer,16929101
BALBES,18094476
XDS,20124692
PHENIX,20124702
CCP4,21460441
Refmac,21460454
CCP4mg,21460457
"PDB-redo database of re-refined PDB entries",22505269
PXImage,15299374
CCPEM,28580908
DIALS,29533234
CNSsolve,9757107
elastix,19923044
"mRMR Feature Selection",16119262
"Services from Zhou Laboratory",12381853
NetMHC,12717023
LipoP,12876315
SSP,17088319
ChloroP,10338008
CLUMPAK,25684545
Metaxa2,25732605
pophelper,26850166
GControl,11315092
BAYESFST,15012769
MapMan,14996223
"MITOPROT II",8944766
SLP,20236171
aPPRove,21557747
msatcommander,21585724
Arlequin,21565059
Stacks,23701397
"UNITE rDNA",24112409
Oufti,26538279
Mercator,24237261
qtlseq,23289725
Araport,27862469
"IMCB - Fugu Genome Project",12142439
Rescue-ESE,12114529
GemTools,12493913
RosettaDesign,14631033
ImmunoDB,17588928
PLATA,18566288
GLOBETROTTER,24531965
"The Human Protein Atlas",25613900
DrEdGE,1899488
COILS,2031185
"SAGE Home Page",7570003
DRAWID,9302295
COGs,9381173
"DExSI: Targeted GC-MS Metabolomics",9360933
NGSCheckMate,2836952
"Gibbs Motif Sampler",8211139
3d-dna,28336562
NetPhorest,18765831
plasmidfinder,24777092
mothur,19801464
SiteEngine,1514784
Macrel,338490
PhosPhAt,80383
Gplas,334726
MACARON,97269
NDtree,24574290
MLST,22238442
iRSpot-Pse6NC2.0,163377
Sequedex,229252
SimPlot,9847317
Align-GVGD,16014699
MirGeneDB,26473382
BioAFMviewer,332066
MACH2QTL,19715440
Genevestigator,19956698
TANRIC,26208906
HTR,12037407
UNPHASED,18382088
SAM,22127579
gage,19473525
BSMAP,19635165
NetMHCII,19765293
"BLAST (EBI)",20003500
GOrilla,19192299
CNV-seq,19267900
DeconTools,19292916
"BS Seeker",20416082
GWAMA,20509871
"Repeat Explorer",20633259
PeakAnalyzer,20691053
baySeq,20698981
SolexaQA,20875133
MAPSCI,20051126
ShoRAH,21521499
BRENDA,21205310
BRENDA,21261995
rsem,21816040
PASHA,21269502
Mulcom,21276213
Krona,21961884
Blasr,22988817
PANDAseq,22333067
"Atlas Suite",22239737
EpiDISH,22568884
Perseus,23176165
Enrichr,23586463
MIMO,23323971
AUREA,23323831
Skewer,24925680
PLEK,25239089
SVMHC,11869452
EasyGene,12525261
MUSCLE,15318951
SNAP,15144565
PPS,15212693
MLST-DB,15230973
Kalign,16343337
Exonerate,15713233
COLOMBO,16542435
TreeDyn,17032440
AUGUSTUS,16469098
ARACNE,16723010
"CRISPRs Database",17521438
"GTOM - Generalized Topological Overlaping Measure",17250769
NNN,17254353
MetaQTL,17207271
NetCTL,17973982
RMAP,18307793
MG-RAST,18803844
PredGPI,18811934
iRefIndex,18215316
minet,18959772
USeq,19061503
WGCNA,19114008
BMGE,20626897
Phylogeny.fr,20067610
"BLAST Ring Image Generator",21205322
"BLAST Ring Image Generator",21824423
MetaPhyler,21989143
CpGAVAS,23256920
"Predicted Prokaryotic Regulatory Proteins (P2RP)",23324311
methylumi,23631413
AlgaePath,24382143
r-ngsplot,24735413
FImpute,24935670
IUTA,24479613
BioVenn,18925949
RAST,18261238
SecretomeP,16212653
BepiPred,16635264
GeneGA,22115189
CONTIGuator,21693004
"BioModels database",20587024
COBRApy,23927696
PrognoScan,19393097
ACPYPE,22824207
DMRcate,25972926
"Open Babel",21982300
Avogadro,22889332
SOAPdenovo2,23587118
Curtain,23870653
ALDEx2,24910773
"Reference Gene Selection",12184808
"The GRID",12620108
"GOMiner WS",12702209
Bioconductor,15461798
pasa,18190707
G-Mo.R-Se,19087247
MACS,18798982
Crossbow,19930550
PEMer,19236709
Bowtie,19261174
Binning,19698104
DESeq,20979621
Quake,21114842
GOseq,20132535
IMAGE,20388197
"The Genomic HyperBrowser",20738864
Cufflinks,21410973
TopHat-Fusion,21835007
PARalyzer,21851591
Cistrome,21859476
bsseq,23034175
methylKit,23034086
Ray,23259615
MAnorm,22424423
tophat2,23618408
WebApollo,24000942
Kraken,24580807
lumpy,24970577
ANGSD,25420514
IPO,25888443
InteractiVenn,25994840
pcaReduce,27005807
EpiDISH,28193155
DrImpute,29884114
"Purge Haplotigs",30497373
iDEP,30567491
bModelTest,28166715
CLARK,25879410
Metagenome-Kin,26261039
km2gcn,28403906
Corset,25063469
ARRmNormalization,25599564
DESeq2,25516281
DETONATE,25608678
Bridger,25723335
LICHeE,25944252
OrthoFinder,26243257
WU-CRISPR,26521937
HiC-Pro,26619908
MAGeCK,26673418
MAST,26653891
cellity,26887813
deconstructSigs,26899170
EAGER,27036623
SCITE,27149953
"CEL-Seq 2",27121950
"1000Genomes VEP",27268795
TanglabCircularRNAPipeline,27315811
CHiCAG,27306882
Mash,27323842
GiniClust,27368803
CRISPOR,27380939
SCZEWAS,27572077
r-mcpcounter,27765066
scDD,27782827
Scoary,27887642
splatter,28899397
r-xcell,29141660
SCANPY,29409532
RaGOO,31661016
sctransform,31870423
tb-profiler,26019726
"Cancer Genome Interpreter (CGI)",29592813
MetFrag,26834843
Rcorrector,26500767
r-virfinder,28683828
MetaWRAP,30219103
"LIPID MAPS",15722563
circBase,25234927
RNAhybrid,15383676
"CyTOF workflow",28663787
"CyTOF workflow",28663787
"CyTOF workflow",28663787
ReactomeFIViz,25309732
ReactomeFIViz,25309732
khmer,26535114
HiCUP,26835000
tximport,26925227
tximport,26925227
"CoNet app",27853510
"CoNet app",27853510
scran,27909575
scran,27909575
Caserel,20940837
PeakFinder,15309048
iHS,16494531
enrichment,17381235
LocARNA,17432929
N-score,18225943
Metastats,19360128
SHRiMP,19461883
VarDom,20862303
GERP++,21152010
DeFuse,21625565
HMMER3,22039361
CoNet,22807668
sparcc,23028285
CAVER,23093919
DiscoTope,23300419
GenomicAlignments,23950696
GEMINI,23874191
PredictSNP,24453961
"BEAST 2",24722319
Clomial,25010360
ClonalFrameML,25675341
BASiCS,26107944
BinPacker,26894997
msprime,27145223
CNVkit,27100738
Unicycler,28594827
OpenMM,28746339
TADbit,28723903
mixomics,29099853
MUMmer,29373581
LASSI,31634364
eigensoft,17194218
sva,17907809
MSTMap,18846212
GAST,19023400
IMPUTE2,19543373
MIXSCORE,21541012
ChromoPainter,22291602
TreeMix,23166502
eQtlBma,23671422
unitig-counter,30419019
lorikeet,26418737
"Arabidopsis eFP Browser",17684564
MetaSim,18841204
RADtools,18852878
NetBox,20169195
FastTree,20224823
GENIE3,20927193
"Enrichment Map Cytoscape Plugin",21085593
PoPoolation,21253599
REPET,21304975
DeconSeq,21408061
DirichletMultinomial,22319561
MultiPhen,22567092
A5,23028432
PROVEAN,23056405
iSNO-PseAAC,23409062
phyloseq,23630581
SNP2HLA,23762245
diffReps,23762400
LAMP,23825543
PathogenFinder,24204795
MethBase,24324667
REPET,24786468
HighMap,24905985
HemI,25372567
SARTools,27280887
seqkit,27706213
EffectiveT3,19390696
STADEN,10547834
SIAMCAT,25432777
IMPUTE2,22384356
DOQTL,25237114
r-blockfest,18780740
MIGRATE,20176979
bcftools_view,23051646
AdmixTools,22960212
alder,23410830
fastSTRUCTURE,24700103
Pse-Analysis,28076851
iACP,26942877
SnpSift,22435069
metawatt,23227024
elastix,24474917
"Diffusion Imaging in Python (DIPY)",24600385
Flexbar,24832523
4mCpred-EL,31661923
iRSpot-TNCPseAAC,24469313
iPPBS-Opt,26797600
VIPERdb,1620571
snpEff,22728672
"The Cancer Genome Atlas API",25691825
Mfuzz,18084642
EPISFA,869348
PPISURV,86313
PRODIGY,26193119
r-epic,29130882
cisTEM,29513216
DeepPoseKit,31570119
GraPhlAn,26157614
Swarm,26713226
AMAS,26835189
iSNO-AAPair,24109555
Phylosift,24482762
VSEARCH,27781170
scikit-image,25024921
D-GENIES,29888139
Swarm,25276506
GroopM,25289188
"MetaBAT 2",31388474
virsorter,26038737