# | Title | Journal | Year | Citations |
---|
1 | Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set | Computational Materials Science | 1996 | 54,900 |
2 | The Sequence Alignment/Map format and SAMtools | Bioinformatics | 2009 | 49,124 |
3 | Trimmomatic: a flexible trimmer for Illumina sequence data | Bioinformatics | 2014 | 46,646 |
4 | Fast and accurate short read alignment with Burrows–Wheeler transform | Bioinformatics | 2009 | 43,062 |
5 | UCSF Chimera?A visualization system for exploratory research and analysis | Journal of Computational Chemistry | 2004 | 37,095 |
6 | STAR: ultrafast universal RNA-seq aligner | Bioinformatics | 2013 | 35,376 |
7 | Fast Parallel Algorithms for Short-Range Molecular Dynamics | Journal of Computational Physics | 1995 | 35,279 |
8 | edgeR: a Bioconductor package for differential expression analysis of digital gene expression data | Bioinformatics | 2010 | 32,955 |
9 | RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies | Bioinformatics | 2014 | 26,744 |
10 | MrBayes 3: Bayesian phylogenetic inference under mixed models | Bioinformatics | 2003 | 26,519 |
11 | Clustal W and Clustal X version 2.0 | Bioinformatics | 2007 | 25,174 |
12 | Semiempirical GGA-type density functional constructed with a long-range dispersion correction | Journal of Computational Chemistry | 2006 | 24,222 |
13 | Multiwfn: A multifunctional wavefunction analyzer | Journal of Computational Chemistry | 2012 | 21,818 |
14 | AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading | Journal of Computational Chemistry | 2010 | 21,573 |
15 | BEDTools: a flexible suite of utilities for comparing genomic features | Bioinformatics | 2010 | 20,367 |
16 | SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing | Journal of Computational Biology | 2012 | 20,193 |
17 | MRBAYES: Bayesian inference of phylogenetic trees | Bioinformatics | 2001 | 20,154 |
18 | General atomic and molecular electronic structure system | Journal of Computational Chemistry | 1993 | 19,020 |
19 | MODELTEST: testing the model of DNA substitution | Bioinformatics | 1998 | 18,761 |
20 | Search and clustering orders of magnitude faster than BLAST | Bioinformatics | 2010 | 18,572 |
21 | Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes | Journal of Computational Physics | 1977 | 18,418 |
22 | HTSeq—a Python framework to work with high-throughput sequencing data | Bioinformatics | 2015 | 17,270 |
23 | AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility | Journal of Computational Chemistry | 2009 | 16,850 |
24 | featureCounts: an efficient general purpose program for assigning sequence reads to genomic features | Bioinformatics | 2014 | 16,839 |
25 | Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data | Bioinformatics | 2012 | 16,096 |
26 | Effect of the damping function in dispersion corrected density functional theory | Journal of Computational Chemistry | 2011 | 15,980 |
27 | Scalable molecular dynamics with NAMD | Journal of Computational Chemistry | 2005 | 15,208 |
28 | RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models | Bioinformatics | 2006 | 14,675 |
29 | Development and testing of a general amber force field | Journal of Computational Chemistry | 2004 | 14,342 |
30 | The Structure and Function of Complex Networks | SIAM Review | 2003 | 14,326 |
31 | CHARMM: A program for macromolecular energy, minimization, and dynamics calculations | Journal of Computational Chemistry | 1983 | 14,316 |
32 | GROMACS: Fast, flexible, and free | Journal of Computational Chemistry | 2005 | 13,676 |
33 | DnaSP v5: a software for comprehensive analysis of DNA polymorphism data | Bioinformatics | 2009 | 13,645 |
34 | LINCS: A linear constraint solver for molecular simulations | Journal of Computational Chemistry | 1997 | 13,446 |
35 | UCHIME improves sensitivity and speed of chimera detection | Bioinformatics | 2011 | 13,241 |
36 | Haploview: analysis and visualization of LD and haplotype maps | Bioinformatics | 2005 | 13,223 |
37 | Prokka: rapid prokaryotic genome annotation | Bioinformatics | 2014 | 12,881 |
38 | Silhouettes: A graphical aid to the interpretation and validation of cluster analysis | Journal of Computational and Applied Mathematics | 1987 | 12,746 |
39 | Volume of fluid (VOF) method for the dynamics of free boundaries | Journal of Computational Physics | 1981 | 12,164 |
40 | Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations | Journal of Computational Physics | 1988 | 11,578 |
41 | FLASH: fast length adjustment of short reads to improve genome assemblies | Bioinformatics | 2011 | 11,573 |
42 | The variant call format and VCFtools | Bioinformatics | 2011 | 11,326 |
43 | TopHat: discovering splice junctions with RNA-Seq | Bioinformatics | 2009 | 11,265 |
44 | fastp: an ultra-fast all-in-one FASTQ preprocessor | Bioinformatics | 2018 | 11,005 |
45 | GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update | Bioinformatics | 2012 | 10,741 |
46 | APE: Analyses of Phylogenetics and Evolution in R language | Bioinformatics | 2004 | 10,601 |
47 | Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research | Bioinformatics | 2005 | 10,566 |
48 | Fast and accurate long-read alignment with Burrows–Wheeler transform | Bioinformatics | 2010 | 10,002 |
49 | Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments | Statistical Applications in Genetics and Molecular Biology | 2004 | 9,992 |
50 | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | Bioinformatics | 2015 | 9,712 |
51 | The ORCA program system | Wiley Interdisciplinary Reviews: Computational Molecular Science | 2012 | 9,098 |
52 | An algorithm for the machine calculation of complex Fourier series | Mathematics of Computation | 1965 | 8,978 |
53 | Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences | Bioinformatics | 2006 | 8,965 |
54 | Chemistry with ADF | Journal of Computational Chemistry | 2001 | 8,854 |
55 | Approximate Riemann solvers, parameter vectors, and difference schemes | Journal of Computational Physics | 1981 | 8,613 |
56 | A perfectly matched layer for the absorption of electromagnetic waves | Journal of Computational Physics | 1994 | 8,574 |
57 | Jalview Version 2—a multiple sequence alignment editor and analysis workbench | Bioinformatics | 2009 | 8,091 |
58 | trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses | Bioinformatics | 2009 | 7,974 |
59 | Minimap2: pairwise alignment for nucleotide sequences | Bioinformatics | 2018 | 7,764 |
60 | The Amber biomolecular simulation programs | Journal of Computational Chemistry | 2005 | 7,742 |
61 | A fast and robust algorithm for Bader decomposition of charge density | Computational Materials Science | 2006 | 7,727 |
62 | A continuum method for modeling surface tension | Journal of Computational Physics | 1992 | 7,608 |
63 | A comparison of normalization methods for high density oligonucleotide array data based on variance and bias | Bioinformatics | 2003 | 7,383 |
64 | Optimization of parameters for semiempirical methods I. Method | Journal of Computational Chemistry | 1989 | 7,369 |
65 | Tensor Decompositions and Applications | SIAM Review | 2009 | 7,108 |
66 | CHARMM: The biomolecular simulation program | Journal of Computational Chemistry | 2009 | 7,077 |
67 | CD-HIT: accelerated for clustering the next-generation sequencing data | Bioinformatics | 2012 | 7,030 |
68 | QUAST: quality assessment tool for genome assemblies | Bioinformatics | 2013 | 6,983 |
69 | Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model | Journal of Computational Chemistry | 2003 | 6,758 |
70 | Power-Law Distributions in Empirical Data | SIAM Review | 2009 | 6,595 |
71 | InterProScan 5: genome-scale protein function classification | Bioinformatics | 2014 | 6,553 |
72 | The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling | Bioinformatics | 2006 | 6,515 |
73 | TASSEL: software for association mapping of complex traits in diverse samples | Bioinformatics | 2007 | 6,407 |
74 | Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F | Journal of Computational Chemistry | 1983 | 6,294 |
75 | Fractional Brownian Motions, Fractional Noises and Applications | SIAM Review | 1968 | 6,147 |
76 | Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models | Journal of Computational Chemistry | 1992 | 6,106 |
77 | GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | Bioinformatics | 2013 | 6,072 |
78 | adegenet: a R package for the multivariate analysis of genetic markers | Bioinformatics | 2008 | 5,999 |
79 | Towards the ultimate conservative difference scheme. V. A second-order sequel to Godunov's method | Journal of Computational Physics | 1979 | 5,957 |
80 | Complex heatmaps reveal patterns and correlations in multidimensional genomic data | Bioinformatics | 2016 | 5,891 |
81 | PACKMOL: A package for building initial configurations for molecular dynamics simulations | Journal of Computational Chemistry | 2009 | 5,831 |
82 | THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Journal of Computational Chemistry | 1992 | 5,736 |
83 | DnaSP, DNA polymorphism analyses by the coalescent and other methods | Bioinformatics | 2003 | 5,561 |
84 | Muiltiobjective Optimization Using Nondominated Sorting in Genetic Algorithms | Evolutionary Computation | 1994 | 5,518 |
85 | A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data | Bioinformatics | 2011 | 5,467 |
86 | CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure | Bioinformatics | 2007 | 5,408 |
87 | CHARMM‐GUI: A web‐based graphical user interface for CHARMM | Journal of Computational Chemistry | 2008 | 5,402 |
88 | ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks | Bioinformatics | 2009 | 5,348 |
89 | Tree View: An application to display phylogenetic trees on personal computers | Bioinformatics | 1996 | 5,235 |
90 | Compact finite difference schemes with spectral-like resolution | Journal of Computational Physics | 1992 | 5,222 |
91 | Efficient Implementation of Weighted ENO Schemes | Journal of Computational Physics | 1996 | 5,195 |
92 | ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R | Bioinformatics | 2019 | 5,128 |
93 | MEGA2: molecular evolutionary genetics analysis software | Bioinformatics | 2001 | 5,102 |
94 | A general method for numerically simulating the stochastic time evolution of coupled chemical reactions | Journal of Computational Physics | 1976 | 5,049 |
95 | Atomic Decomposition by Basis Pursuit | SIAM Journal of Scientific Computing | 1998 | 4,968 |
96 | Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations | Journal of Computational Physics | 2019 | 4,963 |
97 | Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling | Journal of Computational Physics | 1977 | 4,897 |
98 | The rapid generation of mutation data matrices from protein sequences | Bioinformatics | 1992 | 4,891 |
99 | Profile hidden Markov models | Bioinformatics | 1998 | 4,873 |
100 | MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | Bioinformatics | 2015 | 4,864 |