Topic · Genome Rearrangement Algorithms
Most cited papers in Genome Rearrangement Algorithms
What are the most cited papers in Genome Rearrangement Algorithms?
The most cited paper in Genome Rearrangement Algorithms is "Fast and accurate short read alignment with Burrows–Wheeler transform" (Heng Li, Richard M. Durbin, 2009), with 63,989 citations. Next come "BLAST+: architecture and applications" (24,075) and "FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments" (16,398).
Showing 50 of 99 papers. Every paper with more than 449 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Fast and accurate short read alignment with Burrows–Wheeler transform Heng Li, Richard M. Durbin · Bioinformatics | 18 May 2009 | 63,989 |
| 2 | BLAST+: architecture and applications Christiam Camacho, George Coulouris, Vahram Avagyan et al. · BMC Bioinformatics | Dec 2009 | 24,075 |
| 3 | FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Morgan N. Price, Paramvir Dehal, Adam P. Arkin · PLoS ONE | 9 Mar 2010 | 16,398 |
| 4 | FLASH: fast length adjustment of short reads to improve genome assemblies Tanja Magoč, Steven L. Salzberg · Bioinformatics | 7 Sep 2011 | 16,123 |
| 5 | RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Alexandros Stamatakis · Bioinformatics | 23 Aug 2006 | 16,023 |
| 6 | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Felipe A. Simão, Robert Michael Waterhouse, Panagiotis Ioannidis et al. · Bioinformatics | 9 Jun 2015 | 14,906 |
| 7 | trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón · Bioinformatics | 8 Jun 2009 | 14,201 |
| 8 | BEAST: Bayesian evolutionary analysis by sampling trees Alexei J. Drummond, Andrew Rambaut · BMC Evolutionary Biology | 2007 | 13,219 |
| 9 | QUAST: quality assessment tool for genome assemblies Alexey A. Gurevich, Vladislav Saveliev, Nikolay Vyahhi et al. · Bioinformatics | 19 Feb 2013 | 11,980 |
| 10 | Genome sequence-based species delimitation with confidence intervals and improved distance functions Jan P. Meier‐Kolthoff, Alexander F. Auch, Hans-Peter Klenk et al. · BMC Bioinformatics | 21 Feb 2013 | 6,885 |
| 11 | GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Pierre-Alain Chaumeil, Aaron James Mussig, Philip Hugenholtz et al. · Bioinformatics | 14 Nov 2019 | 5,727 |
| 12 | SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler Ruibang Luo et al. · GigaScience | Dec 2012 | 5,718 |
| 13 | A fast, lock-free approach for efficient parallel counting of occurrences of k -mers Guillaume Marçais, Carl Kingsford · Bioinformatics | 7 Jan 2011 | 5,222 |
| 14 | RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Alexey M. Kozlov, Diego Darriba, Tomáš Flouri et al. · Bioinformatics | 24 Apr 2019 | 4,725 |
| 15 | The COG database: an updated version includes eukaryotes Roman L. Tatusov, Natalie D. Fedorova, John D. Jackson et al. · BMC Bioinformatics | 11 Sep 2003 | 4,563 |
| 16 | progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement Aaron E. Darling, Bob Mau, Nicole T. Perna · PLoS ONE | 25 Jun 2010 | 4,152 |
| 17 | Gene finding in novel genomes Ian F. Korf · BMC Bioinformatics | 14 May 2004 | 3,584 |
| 18 | BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons Nabil-Fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour et al. · BMC Genomics | 8 Aug 2011 | 3,494 |
| 19 | Automated generation of heuristics for biological sequence comparison Guy Slater, Ewan Birney · BMC Bioinformatics | 15 Feb 2005 | 3,236 |
| 20 | Inferring Phylogenies. Stephen Wooding · The American Journal of Human Genetics | 16 Apr 2004 | 3,062 |
| 21 | JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison Michael Richter, Ramon A. Rossello-Mora, Frank Oliver Glöckner et al. · Bioinformatics | 16 Nov 2015 | 3,022 |
| 22 | VISTA: computational tools for comparative genomics Kelly A. Frazer, Lior S. Pachter, Alexandre Poliakov et al. · Nucleic Acids Research | Jul 2004 | 3,018 |
| 23 | ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees Chao Zhang, Maryam Rabiee, Erfan Sayyari et al. · BMC Bioinformatics | May 2018 | 2,842 |
| 24 | DELLY: structural variant discovery by integrated paired-end and split-read analysis Tobias Rausch, Thomas Zichner, Andreas Schlattl et al. · Bioinformatics | 3 Sep 2012 | 2,808 |
| 25 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding Mario Stanke, Mark E. Diekhans, Robert Baertsch et al. · Bioinformatics | 24 Jan 2008 | 2,677 |
| 26 | Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices Olga Chernomor, Arndt von Haeseler, Bùi Quang Minh · Systematic Biology | 26 Apr 2016 | 2,428 |
| 27 | De novo identification of repeat families in large genomes Alkes L. Price, Natalie C. Jones, Pavel A. Pevzner · Computer applications in the biosciences | Jun 2005 | 2,356 |
| 28 | CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes Genı́s Parra, Keith Bradnam, Ian F. Korf · Bioinformatics | Mar 2007 | 2,349 |
| 29 | CAFE: a computational tool for the study of gene family evolution Tijl De Bie, Nello Cristianini, Jeffery P. Demuth et al. · Bioinformatics | 16 Mar 2006 | 2,100 |
| 30 | KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Takuya Aramaki, Romain Blanc‐Mathieu, Hisashi Endo et al. · Bioinformatics | 18 Nov 2019 | 2,089 |
| 31 | CONSEL: for assessing the confidence of phylogenetic tree selection Hidetoshi Shimodaira, Masami Hasegawa · Bioinformatics | Dec 2001 | 2,085 |
| 32 | GenomeScope: fast reference-free genome profiling from short reads Gregory W. Vurture, Fritz Joachim Sedlazeck, Maria Nattestad et al. · Bioinformatics | 17 Mar 2017 | 2,040 |
| 33 | LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons David Ellinghaus, Stefan Kurtz, Ute Willhoeft · BMC Bioinformatics | 14 Jan 2008 | 1,830 |
| 34 | BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments Alexis Criscuolo, Simonetta Gribaldo · BMC Evolutionary Biology | 2010 | 1,799 |
| 35 | clinker & clustermap.js: automatic generation of gene cluster comparison figures Cameron L. M. Gilchrist, Yit‐Heng Chooi · Bioinformatics | 6 Jan 2021 | 1,750 |
| 36 | Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees Andrew Rambaut, N. Grass · Computer applications in the biosciences | 1997 | 1,723 |
| 37 | Versatile genome assembly evaluation with QUAST-LG Alla Mikheenko, Andrey D. Prjibelski, Vladislav Saveliev et al. · Bioinformatics | 12 Apr 2018 | 1,709 |
| 38 | The MaSuRCA genome assembler Aleksey V. Zimin, Guillaume Marçais, Daniela Puiu et al. · Bioinformatics | 29 Aug 2013 | 1,630 |
| 39 | Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline Shujun Ou, Weija Su, Yi Liao et al. · Genome biology | 16 Dec 2019 | 1,586 |
| 40 | Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern et al. · BMC Bioinformatics | 9 Feb 2006 | 1,478 |
| 41 | Mosdepth: quick coverage calculation for genomes and exomes Brent S. Pedersen, Aaron R. Quinlan · Bioinformatics | 30 Oct 2017 | 1,401 |
| 42 | NextPolish: a fast and efficient genome polishing tool for long-read assembly Jiang Yong Hu, Junpeng Fan, Zongyi Sun et al. · Bioinformatics | 26 Nov 2019 | 1,349 |
| 43 | Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs Giulio Formenti, Linelle Ann L. Abueg, Angelo Brajuka et al. · Bioinformatics | 7 Jul 2022 | 1,275 |
| 44 | Optimal alignments in linear space Eugene Wimberly Myers, Webb Miller · Computer applications in the biosciences | 1988 | 1,252 |
| 45 | IRscope: an online program to visualize the junction sites of chloroplast genomes Ali Amiryousefi, Jaakko Hyvönen, Péter Poczai · Bioinformatics | 4 Apr 2018 | 1,245 |
| 46 | A whole-genome assembly of the domestic cow, Bos taurus Aleksey V. Zimin, Arthur L. Delcher, Liliana Florea et al. · Genome biology | 24 Apr 2009 | 1,210 |
| 47 | Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck et al. · Bioinformatics | 22 Jan 2004 | 1,187 |
| 48 | A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Eugene V. Koonin, Natalie D. Fedorova, John D. Jackson et al. · Genome biology | 15 Jan 2004 | 1,147 |
| 49 | nhmmer: DNA homology search with profile HMMs Travis J. Wheeler, Sean R. Eddy · Bioinformatics | 9 Jul 2013 | 1,097 |
| 50 | Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified Thomas Keane, Christopher J. Creevey, Melissa M. Pentony et al. · BMC Evolutionary Biology | 24 Mar 2006 | 1,086 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.