| # | Title | Journal | Year | Citations |
|---|
| 1 | The Sequence Alignment/Map format and SAMtools | Bioinformatics | 2009 | 49,124 |
| 2 | Trimmomatic: a flexible trimmer for Illumina sequence data | Bioinformatics | 2014 | 46,646 |
| 3 | Fast and accurate short read alignment with Burrows–Wheeler transform | Bioinformatics | 2009 | 43,062 |
| 4 | STAR: ultrafast universal RNA-seq aligner | Bioinformatics | 2013 | 35,376 |
| 5 | edgeR: a Bioconductor package for differential expression analysis of digital gene expression data | Bioinformatics | 2010 | 32,955 |
| 6 | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies | Bioinformatics | 2014 | 26,744 |
| 7 | MrBayes 3: Bayesian phylogenetic inference under mixed models | Bioinformatics | 2003 | 26,519 |
| 8 | Clustal W and Clustal X version 2.0 | Bioinformatics | 2007 | 25,174 |
| 9 | BEDTools: a flexible suite of utilities for comparing genomic features | Bioinformatics | 2010 | 20,367 |
| 10 | MRBAYES: Bayesian inference of phylogenetic trees | Bioinformatics | 2001 | 20,154 |
| 11 | MODELTEST: testing the model of DNA substitution | Bioinformatics | 1998 | 18,761 |
| 12 | Search and clustering orders of magnitude faster than BLAST | Bioinformatics | 2010 | 18,572 |
| 13 | HTSeq—a Python framework to work with high-throughput sequencing data | Bioinformatics | 2015 | 17,270 |
| 14 | featureCounts: an efficient general purpose program for assigning sequence reads to genomic features | Bioinformatics | 2014 | 16,839 |
| 15 | Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data | Bioinformatics | 2012 | 16,096 |
| 16 | RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models | Bioinformatics | 2006 | 14,675 |
| 17 | DnaSP v5: a software for comprehensive analysis of DNA polymorphism data | Bioinformatics | 2009 | 13,645 |
| 18 | UCHIME improves sensitivity and speed of chimera detection | Bioinformatics | 2011 | 13,241 |
| 19 | Haploview: analysis and visualization of LD and haplotype maps | Bioinformatics | 2005 | 13,223 |
| 20 | Prokka: rapid prokaryotic genome annotation | Bioinformatics | 2014 | 12,881 |
| 21 | FLASH: fast length adjustment of short reads to improve genome assemblies | Bioinformatics | 2011 | 11,573 |
| 22 | The variant call format and VCFtools | Bioinformatics | 2011 | 11,326 |
| 23 | TopHat: discovering splice junctions with RNA-Seq | Bioinformatics | 2009 | 11,265 |
| 24 | fastp: an ultra-fast all-in-one FASTQ preprocessor | Bioinformatics | 2018 | 11,005 |
| 25 | GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update | Bioinformatics | 2012 | 10,741 |
| 26 | APE: Analyses of Phylogenetics and Evolution in R language | Bioinformatics | 2004 | 10,601 |
| 27 | Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research | Bioinformatics | 2005 | 10,566 |
| 28 | Fast and accurate long-read alignment with Burrows–Wheeler transform | Bioinformatics | 2010 | 10,002 |
| 29 | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | Bioinformatics | 2015 | 9,712 |
| 30 | Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences | Bioinformatics | 2006 | 8,965 |
| 31 | Jalview Version 2—a multiple sequence alignment editor and analysis workbench | Bioinformatics | 2009 | 8,091 |
| 32 | trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses | Bioinformatics | 2009 | 7,974 |
| 33 | Minimap2: pairwise alignment for nucleotide sequences | Bioinformatics | 2018 | 7,764 |
| 34 | A comparison of normalization methods for high density oligonucleotide array data based on variance and bias | Bioinformatics | 2003 | 7,383 |
| 35 | CD-HIT: accelerated for clustering the next-generation sequencing data | Bioinformatics | 2012 | 7,030 |
| 36 | QUAST: quality assessment tool for genome assemblies | Bioinformatics | 2013 | 6,983 |
| 37 | InterProScan 5: genome-scale protein function classification | Bioinformatics | 2014 | 6,553 |
| 38 | The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling | Bioinformatics | 2006 | 6,515 |
| 39 | TASSEL: software for association mapping of complex traits in diverse samples | Bioinformatics | 2007 | 6,407 |
| 40 | GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | Bioinformatics | 2013 | 6,072 |
| 41 | adegenet: a R package for the multivariate analysis of genetic markers | Bioinformatics | 2008 | 5,999 |
| 42 | Complex heatmaps reveal patterns and correlations in multidimensional genomic data | Bioinformatics | 2016 | 5,891 |
| 43 | DnaSP, DNA polymorphism analyses by the coalescent and other methods | Bioinformatics | 2003 | 5,561 |
| 44 | A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data | Bioinformatics | 2011 | 5,467 |
| 45 | CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure | Bioinformatics | 2007 | 5,408 |
| 46 | ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks | Bioinformatics | 2009 | 5,348 |
| 47 | Tree View: An application to display phylogenetic trees on personal computers | Bioinformatics | 1996 | 5,235 |
| 48 | ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R | Bioinformatics | 2019 | 5,128 |
| 49 | MEGA2: molecular evolutionary genetics analysis software | Bioinformatics | 2001 | 5,102 |
| 50 | The rapid generation of mutation data matrices from protein sequences | Bioinformatics | 1992 | 4,891 |
