A citation-based method for searching scientific literature

Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
Times Cited: 19826







List of co-cited articles
147 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity



Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk, Markus Göker. BMC Bioinformatics 2013
11



MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A Suchard, John P Huelsenbeck. Syst Biol 2012
8



TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R Thomas, Margaret H Frank, Yehua He, Rui Xia. Mol Plant 2020
8

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun. Int J Syst Evol Microbiol 2017
7


MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
7


DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.
Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio, Sara Guirao-Rico, Pablo Librado, Sebastián E Ramos-Onsins, Alejandro Sánchez-Gracia. Mol Biol Evol 2017
6

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
6

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
6

The RAST Server: rapid annotations using subsystems technology.
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal,[...]. BMC Genomics 2008
6

jModelTest 2: more models, new heuristics and parallel computing.
Diego Darriba, Guillermo L Taboada, Ramón Doallo, David Posada. Nat Methods 2012
6



JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison.
Michael Richter, Ramon Rosselló-Móra, Frank Oliver Glöckner, Jörg Peplies. Bioinformatics 2016
5

NCBI prokaryotic genome annotation pipeline.
Tatiana Tatusova, Michael DiCuccio, Azat Badretdin, Vyacheslav Chetvernin, Eric P Nawrocki, Leonid Zaslavsky, Alexandre Lomsadze, Kim D Pruitt, Mark Borodovsky, James Ostell. Nucleic Acids Res 2016
5

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. Syst Biol 2010
5

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Matthew Kearse, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, Alex Cooper, Sidney Markowitz, Chris Duran,[...]. Bioinformatics 2012
5

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard. Syst Biol 2018
5

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
5

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
5

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts. Nucleic Acids Res 2002
5

GSDS 2.0: an upgraded gene feature visualization server.
Bo Hu, Jinpu Jin, An-Yuan Guo, He Zhang, Jingchu Luo, Ge Gao. Bioinformatics 2015
5

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
Johan Goris, Konstantinos T Konstantinidis, Joel A Klappenbach, Tom Coenye, Peter Vandamme, James M Tiedje. Int J Syst Evol Microbiol 2007
5

A large-scale evaluation of algorithms to calculate average nucleotide identity.
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun. Antonie Van Leeuwenhoek 2017
5


MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
Yupeng Wang, Haibao Tang, Jeremy D Debarry, Xu Tan, Jingping Li, Xiyin Wang, Tae-ho Lee, Huizhe Jin, Barry Marler, Hui Guo,[...]. Nucleic Acids Res 2012
4

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
4

OrthoANI: An improved algorithm and software for calculating average nucleotide identity.
Imchang Lee, Yeong Ouk Kim, Sang-Cheol Park, Jongsik Chun. Int J Syst Evol Microbiol 2016
4

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.
Kai Blin, Simon Shaw, Katharina Steinke, Rasmus Villebro, Nadine Ziemert, Sang Yup Lee, Marnix H Medema, Tilmann Weber. Nucleic Acids Res 2019
4

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
J D Thompson, T J Gibson, F Plewniak, F Jeanmougin, D G Higgins. Nucleic Acids Res 1997
3


MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, Takashi Miyata. Nucleic Acids Res 2002
3





The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
3


SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
Brejnev Muhizi Muhire, Arvind Varsani, Darren Patrick Martin. PLoS One 2014
601
3

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A Gurevich, Mikhail Dvorkin, Alexander S Kulikov, Valery M Lesin, Sergey I Nikolenko, Son Pham, Andrey D Prjibelski,[...]. J Comput Biol 2012
3

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
3




Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.