A citation-based method for searching scientific literature

Fredrik Ronquist, John P Huelsenbeck. Bioinformatics 2003
Times Cited: 14541







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



Times Cited
  Times     Co-cited
Similarity




jModelTest 2: more models, new heuristics and parallel computing.
Diego Darriba, Guillermo L Taboada, Ramón Doallo, David Posada. Nat Methods 2012
18

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard. Syst Biol 2018
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
15


MRBAYES: Bayesian inference of phylogenetic trees.
J P Huelsenbeck, F Ronquist. Bioinformatics 2001
13

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
13

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
13


jModelTest: phylogenetic model averaging.
David Posada. Mol Biol Evol 2008
12


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
12

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.
Robert Lanfear, Paul B Frandsen, April M Wright, Tereza Senfeld, Brett Calcott. Mol Biol Evol 2017
11

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
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
11

UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Le Sy Vinh. Mol Biol Evol 2018
10

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

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada. Brief Bioinform 2019
8

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
8


Bayesian phylogenetics with BEAUti and the BEAST 1.7.
Alexei J Drummond, Marc A Suchard, Dong Xie, Andrew Rambaut. Mol Biol Evol 2012
7



Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
Robert Lanfear, Brett Calcott, Simon Y W Ho, Stephane Guindon. Mol Biol Evol 2012
7

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices.
Olga Chernomor, Arndt von Haeseler, Bui Quang Minh. Syst Biol 2016
461
6

MITOS: improved de novo metazoan mitochondrial genome annotation.
Matthias Bernt, Alexander Donath, Frank Jühling, Fabian Externbrink, Catherine Florentz, Guido Fritzsch, Joern Pütz, Martin Middendorf, Peter F Stadler. Mol Phylogenet Evol 2013
6



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
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
6

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.
Jana Trifinopoulos, Lam-Tung Nguyen, Arndt von Haeseler, Bui Quang Minh. Nucleic Acids Res 2016
6



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



Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
5


APE: Analyses of Phylogenetics and Evolution in R language.
Emmanuel Paradis, Julien Claude, Korbinian Strimmer. Bioinformatics 2004
5

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
5


Ultrafast approximation for phylogenetic bootstrap.
Bui Quang Minh, Minh Anh Thi Nguyen, Arndt von Haeseler. Mol Biol Evol 2013
5

PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.
Dong Zhang, Fangluan Gao, Ivan Jakovlić, Hong Zou, Jin Zhang, Wen X Li, Gui T Wang. Mol Ecol Resour 2020
499
5


MODELTEST: testing the model of DNA substitution.
D Posada, K A Crandall. Bioinformatics 1998
5

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
702
4


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
973
4

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
4


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.