| The Sequence Alignment/Map format and SAMtools | 2009/06/08 | English | 36,514 |
| Trimmomatic: a flexible trimmer for Illumina sequence data | 2014/04/01 | English | 35,655 |
| Fast and accurate short read alignment with Burrows–Wheeler transform | 2009/05/18 | English | 30,288 |
| STAR: ultrafast universal RNA-seq aligner | 2012/10/25 | English | 25,304 |
| edgeR: a Bioconductor package for differential expression analysis of digital gene expression data | 2009/11/11 | English | 24,794 |
| Clustal W and Clustal X version 2.0 | 2007/09/10 | English | 21,766 |
| RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies | 2014/01/21 | English | 21,269 |
| MrBayes 3: Bayesian phylogenetic inference under mixed models | 2003/08/12 | English | 19,656 |
| MRBAYES: Bayesian inference of phylogenetic trees | 2001/08/01 | English | 16,639 |
| Search and clustering orders of magnitude faster than BLAST | 2010/08/12 | English | 15,171 |
| BEDTools: a flexible suite of utilities for comparing genomic features | 2010/01/28 | English | 14,377 |
| Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data | 2012/04/27 | English | 13,627 |
| MODELTEST: testing the model of DNA substitution. | 1998/01/01 | English | 13,082 |
| HTSeq—a Python framework to work with high-throughput sequencing data | 2014/09/25 | English | 12,699 |
| featureCounts: an efficient general purpose program for assigning sequence reads to genomic features | 2013/11/13 | English | 12,394 |
| DnaSP v5: a software for comprehensive analysis of DNA polymorphism data | 2009/04/03 | English | 12,184 |
| RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models | 2006/08/23 | English | 12,019 |
| Haploview: analysis and visualization of LD and haplotype maps | 2004/08/05 | English | 11,327 |
| UCHIME improves sensitivity and speed of chimera detection | 2011/06/23 | English | 11,086 |
| Prokka: rapid prokaryotic genome annotation | 2014/03/18 | English | 9,805 |
| FLASH: fast length adjustment of short reads to improve genome assemblies | 2011/09/07 | English | 9,699 |
| fastp: an ultra-fast all-in-one FASTQ preprocessor | 2018/09/01 | English | 9,253 |
| TopHat: discovering splice junctions with RNA-Seq | 2009/03/16 | English | 8,914 |
| Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research | 2005/08/04 | English | 8,714 |
| APE: Analyses of Phylogenetics and Evolution in R language | 2004/01/22 | English | 8,664 |
| The variant call format and VCFtools | 2011/06/07 | English | 8,380 |
| GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update | 2012/07/20 | English | 8,028 |
| Fast and accurate long-read alignment with Burrows–Wheeler transform | 2010/01/15 | English | 7,750 |
| BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | 2015/06/09 | English | 7,409 |
| Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences | 2006/05/26 | English | 6,849 |