Fredrik Ronquist, John P Huelsenbeck. Bioinformatics 2003
Times Cited: 14541
Times Cited: 14541
Times Cited
Times Co-cited
Similarity
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
Kazutaka Katoh, Daron M Standley. Mol Biol Evol 2013
35
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Alexandros Stamatakis. Bioinformatics 2014
Alexandros Stamatakis. Bioinformatics 2014
18
jModelTest 2: more models, new heuristics and parallel computing.
Diego Darriba, Guillermo L Taboada, Ramón Doallo, David Posada. Nat Methods 2012
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
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
Lam-Tung Nguyen, Heiko A Schmidt, Arndt von Haeseler, Bui Quang Minh. Mol Biol Evol 2015
15
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Robert C Edgar. Nucleic Acids Res 2004
Robert C Edgar. Nucleic Acids Res 2004
13
MRBAYES: Bayesian inference of phylogenetic trees.
J P Huelsenbeck, F Ronquist. Bioinformatics 2001
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
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
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
13
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Alexandros Stamatakis. Bioinformatics 2006
Alexandros Stamatakis. Bioinformatics 2006
12
Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species.
R Vilgalys, M Hester. J Bacteriol 1990
R Vilgalys, M Hester. J Bacteriol 1990
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
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
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
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
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
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
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
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
J D Thompson, T J Gibson, F Plewniak, F Jeanmougin, D G Higgins. Nucleic Acids Res 1997
8
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.
P Librado, J Rozas. Bioinformatics 2009
P Librado, J Rozas. Bioinformatics 2009
8
Bayesian phylogenetics with BEAUti and the BEAST 1.7.
Alexei J Drummond, Marc A Suchard, Dong Xie, Andrew Rambaut. Mol Biol Evol 2012
Alexei J Drummond, Marc A Suchard, Dong Xie, Andrew Rambaut. Mol Biol Evol 2012
7
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
J Castresana. Mol Biol Evol 2000
J Castresana. Mol Biol Evol 2000
7
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon, Olivier Gascuel. Syst Biol 2003
Stéphane Guindon, Olivier Gascuel. Syst Biol 2003
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
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
Olga Chernomor, Arndt von Haeseler, Bui Quang Minh. Syst Biol 2016
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
Matthias Bernt, Alexander Donath, Frank Jühling, Fabian Externbrink, Catherine Florentz, Guido Fritzsch, Joern Pütz, Martin Middendorf, Peter F Stadler. Mol Phylogenet Evol 2013
6
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.
Joseph Felsenstein. Evolution 1985
Joseph Felsenstein. Evolution 1985
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
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
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
Jana Trifinopoulos, Lam-Tung Nguyen, Arndt von Haeseler, Bui Quang Minh. Nucleic Acids Res 2016
6
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences.
Dean Laslett, Björn Canbäck. Bioinformatics 2008
Dean Laslett, Björn Canbäck. Bioinformatics 2008
6
ITS primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts.
M Gardes, T D Bruns. Mol Ecol 1993
M Gardes, T D Bruns. Mol Ecol 1993
6
Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
5
Fast and accurate short read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2009
Heng Li, Richard Durbin. Bioinformatics 2009
5
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests.
David Posada, Thomas R Buckley. Syst Biol 2004
David Posada, Thomas R Buckley. Syst Biol 2004
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
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
5
APE: Analyses of Phylogenetics and Evolution in R language.
Emmanuel Paradis, Julien Claude, Korbinian Strimmer. Bioinformatics 2004
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
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
5
Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit.
Y J Liu, S Whelen, B D Hall. Mol Biol Evol 1999
Y J Liu, S Whelen, B D Hall. Mol Biol Evol 1999
5
Ultrafast approximation for phylogenetic bootstrap.
Bui Quang Minh, Minh Anh Thi Nguyen, Arndt von Haeseler. Mol Biol Evol 2013
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
Dong Zhang, Fangluan Gao, Ivan Jakovlić, Hong Zou, Jin Zhang, Wen X Li, Gui T Wang. Mol Ecol Resour 2020
5
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Gerard Talavera, Jose Castresana. Syst Biol 2007
Gerard Talavera, Jose Castresana. Syst Biol 2007
5
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
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
4
DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.
O Folmer, M Black, W Hoeh, R Lutz, R Vrijenhoek. Mol Mar Biol Biotechnol 1994
O Folmer, M Black, W Hoeh, R Lutz, R Vrijenhoek. Mol Mar Biol Biotechnol 1994
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
Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut. Virus Evol 2018
4
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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.