| Jalview Version 2—a multiple sequence alignment editor and analysis workbench | 2009/01/16 | English | 6,393 |
| trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses | 2009/06/08 | English | 6,044 |
| A comparison of normalization methods for high density
oligonucleotide array data based on variance and bias | 2003/01/22 | English | 5,815 |
| The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling | 2005/11/13 | English | 5,592 |
| CD-HIT: accelerated for clustering the next-generation sequencing data | 2012/10/11 | English | 5,453 |
| QUAST: quality assessment tool for genome assemblies | 2013/02/19 | English | 5,394 |
| GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | 2013/02/13 | English | 5,392 |
| adegenet: a R package for the multivariate analysis of genetic markers | 2008/04/08 | English | 5,199 |
| Minimap2: pairwise alignment for nucleotide sequences | 2018/05/10 | English | 5,059 |
| TASSEL: software for association mapping of complex traits in diverse samples | 2007/06/22 | English | 4,915 |
| DnaSP, DNA polymorphism analyses by the coalescent and other methods | 2003/12/12 | English | 4,812 |
| CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure | 2007/05/07 | English | 4,802 |
| InterProScan 5: genome-scale protein function classification | 2014/01/29 | English | 4,766 |
| Complex heatmaps reveal patterns and correlations in multidimensional genomic data | 2016/05/20 | English | 4,404 |
| ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks | 2009/02/23 | English | 4,174 |
| ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R | 2018/07/17 | English | 4,112 |
| MEGA2: molecular evolutionary genetics analysis software | 2001/12/01 | English | 4,005 |
| Picante: R tools for integrating phylogenies and ecology | 2010/04/15 | English | 3,914 |
| A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data | 2011/09/08 | English | 3,789 |
| affy—analysis of Affymetrix GeneChip data at the probe level | 2004/02/12 | English | 3,744 |
| MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | 2015/01/20 | English | 3,707 |
| Molecular signatures database (MSigDB) 3.0 | 2011/05/05 | English | 3,473 |
| Causal analysis approaches in Ingenuity Pathway Analysis | 2013/12/13 | English | 3,463 |
| Profile hidden Markov models. | 1998/01/01 | English | 3,429 |
| Quality control and preprocessing of metagenomic datasets | 2011/01/28 | English | 3,391 |
| Cytoscape 2.8: new features for data integration and network visualization | 2010/12/12 | English | 3,299 |
| MultiQC: summarize analysis results for multiple tools and samples in a single report | 2016/06/16 | English | 3,298 |
| Skyline: an open source document editor for creating and analyzing targeted proteomics experiments | 2010/02/09 | English | 3,173 |
| PowerMarker: an integrated analysis environment for genetic marker analysis | 2005/02/10 | English | 3,123 |
| DEGseq: an R package for identifying differentially expressed genes from RNA-seq data | 2009/10/24 | English | 3,080 |