| WGCNA: an R package for weighted correlation network analysis | 2008/12/01 | English | 12,981 |
| RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome | 2011/08/04 | English | 12,653 |
| BLAST+: architecture and applications | 2009/12/01 | English | 11,184 |
| pROC: an open-source package for R and S+ to analyze and compare ROC curves | 2011/03/17 | English | 7,111 |
| GSVA: gene set variation analysis for microarray and RNA-Seq data | 2013/01/16 | English | 6,537 |
| Prodigal: prokaryotic gene recognition and translation initiation site identification | 2010/03/08 | English | 6,339 |
| MUSCLE: a multiple sequence alignment method with reduced time and space complexity | 2004/08/19 | English | 5,929 |
| Genome sequence-based species delimitation with confidence intervals and improved distance functions | 2013/02/21 | English | 4,726 |
| Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool | 2013/04/15 | English | 3,713 |
| I-TASSER server for protein 3D structure prediction | 2008/01/23 | English | 3,654 |
| ImageJ2: ImageJ for the next generation of scientific image data | 2017/11/29 | English | 3,647 |
| Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction | 2012/06/18 | English | 3,606 |
| An automated method for finding molecular complexes in large protein interaction networks | 2003/01/13 | English | 3,396 |
| The COG database: an updated version includes eukaryotes | 2003/09/11 | English | 3,090 |
| MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data | 2010/07/23 | English | 2,507 |
| The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes | 2008/09/19 | English | 2,391 |
| GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists | 2009/02/03 | English | 2,310 |
| DNA methylation arrays as surrogate measures of cell mixture distribution | 2012/05/08 | English | 2,080 |
| Bias in random forest variable importance measures: Illustrations, sources and a solution | 2007/01/25 | English | 1,901 |
| Gene finding in novel genomes | 2004/05/14 | English | 1,849 |
| Molecular ecological network analyses | 2012/05/30 | English | 1,761 |
| Conditional variable importance for random forests | 2008/07/11 | English | 1,753 |
| Automated generation of heuristics for biological sequence comparison | 2005/02/15 | English | 1,666 |
| BIGSdb: Scalable analysis of bacterial genome variation at the population level | 2010/12/01 | English | 1,614 |
| VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R | 2011/01/26 | English | 1,594 |
| PANDAseq: paired-end assembler for illumina sequences | 2012/02/14 | English | 1,538 |
| Gene selection and classification of microarray data using random forest | 2006/01/06 | English | 1,498 |
| VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines | 2007/01/05 | English | 1,465 |
| Statistical analysis of real-time PCR data | 2006/02/22 | English | 1,407 |
| ANGSD: Analysis of Next Generation Sequencing Data | 2014/11/25 | English | 1,382 |