A citation-based method for searching scientific literature

Darren P Martin, Ben Murrell, Michael Golden, Arjun Khoosal, Brejnev Muhire. Virus Evol 2015
Times Cited: 1729







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



Times Cited
  Times     Co-cited
Similarity


MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
24




Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard. Syst Biol 2018
19

Possible emergence of new geminiviruses by frequent recombination.
M Padidam, S Sawyer, C M Fauquet. Virology 1999
967
19

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
18



An exact nonparametric method for inferring mosaic structure in sequence triplets.
Maciej F Boni, David Posada, Marcus W Feldman. Genetics 2007
535
16

A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.
D P Martin, D Posada, K A Crandall, C Williamson. AIDS Res Hum Retroviruses 2005
580
16

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen).
Andrew Rambaut, Tommy T Lam, Luiz Max Carvalho, Oliver G Pybus. Virus Evol 2016
983
15

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
14

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.
Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut. Virus Evol 2018
14


Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
K S Lole, R C Bollinger, R S Paranjape, D Gadkari, S S Kulkarni, N G Novak, R Ingersoll, H W Sheppard, S C Ray. J Virol 1999
12

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
Brejnev Muhizi Muhire, Arvind Varsani, Darren Patrick Martin. PLoS One 2014
654
9

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski, Sudhir Kumar. Mol Biol Evol 2013
9

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.
Filip Bielejec, Guy Baele, Bram Vrancken, Marc A Suchard, Andrew Rambaut, Philippe Lemey. Mol Biol Evol 2016
234
8

jModelTest 2: more models, new heuristics and parallel computing.
Diego Darriba, Guillermo L Taboada, Ramón Doallo, David Posada. Nat Methods 2012
8

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear. Mol Biol Evol 2020
8

FUBAR: a fast, unconstrained bayesian approximation for inferring selection.
Ben Murrell, Sasha Moola, Amandla Mabona, Thomas Weighill, Daniel Sheward, Sergei L Kosakovsky Pond, Konrad Scheffler. Mol Biol Evol 2013
658
8

Detecting individual sites subject to episodic diversifying selection.
Ben Murrell, Joel O Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, Sergei L Kosakovsky Pond. PLoS Genet 2012
913
8


Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes.
Steven Weaver, Stephen D Shank, Stephanie J Spielman, Michael Li, Spencer V Muse, Sergei L Kosakovsky Pond. Mol Biol Evol 2018
336
8

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.
Guy Baele, Philippe Lemey, Trevor Bedford, Andrew Rambaut, Marc A Suchard, Alexander V Alekseyenko. Mol Biol Evol 2012
661
7

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.
Mandev S Gill, Philippe Lemey, Nuno R Faria, Andrew Rambaut, Beth Shapiro, Marc A Suchard. Mol Biol Evol 2013
297
7

Clustal W and Clustal X version 2.0.
M A Larkin, G Blackshields, N P Brown, R Chenna, P A McGettigan, H McWilliam, F Valentin, I M Wallace, A Wilm, R Lopez,[...]. Bioinformatics 2007
7

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
7

Application of phylogenetic networks in evolutionary studies.
Daniel H Huson, David Bryant. Mol Biol Evol 2006
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
7

Relaxed phylogenetics and dating with confidence.
Alexei J Drummond, Simon Y W Ho, Matthew J Phillips, Andrew Rambaut. PLoS Biol 2006
6

A simple and robust statistical test for detecting the presence of recombination.
Trevor C Bruen, Hervé Philippe, David Bryant. Genetics 2006
837
6

ModelFinder: fast model selection for accurate phylogenetic estimates.
Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, Lars S Jermiin. Nat Methods 2017
6

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Remco Bouckaert, Timothy G Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio,[...]. PLoS Comput Biol 2019
872
6

BEAST: Bayesian evolutionary analysis by sampling trees.
Alexei J Drummond, Andrew Rambaut. BMC Evol Biol 2007
6

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
6


HyPhy: hypothesis testing using phylogenies.
Sergei L Kosakovsky Pond, Simon D W Frost, Spencer V Muse. Bioinformatics 2005
6

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

MEGA11: Molecular Evolutionary Genetics Analysis Version 11.
Koichiro Tamura, Glen Stecher, Sudhir Kumar. Mol Biol Evol 2021
857
6

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
5

Bayesian phylogeography finds its roots.
Philippe Lemey, Andrew Rambaut, Alexei J Drummond, Marc A Suchard. PLoS Comput Biol 2009
5

Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.
M O Salminen, J K Carr, D S Burke, F E McCutchan. AIDS Res Hum Retroviruses 1995
661
5




UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Le Sy Vinh. Mol Biol Evol 2018
5

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
5

The global distribution and burden of dengue.
Samir Bhatt, Peter W Gething, Oliver J Brady, Jane P Messina, Andrew W Farlow, Catherine L Moyes, John M Drake, John S Brownstein, Anne G Hoen, Osman Sankoh,[...]. Nature 2013
5


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.