A citation-based method for searching scientific literature

Bui Quang Minh, Minh Anh Thi Nguyen, Arndt von Haeseler. Mol Biol Evol 2013
Times Cited: 1315







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



Times Cited
  Times     Co-cited
Similarity


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
72

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
54


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
29

UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Le Sy Vinh. Mol Biol Evol 2018
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
16

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
16

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
16

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
15

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
13

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
592
13

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
13


Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.
Maria Anisimova, Manuel Gil, Jean-François Dufayard, Christophe Dessimoz, Olivier Gascuel. Syst Biol 2011
469
10

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
9

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
9

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
8


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
8

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
7

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
7

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
7


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
824
7

A complete domain-to-species taxonomy for Bacteria and Archaea.
Donovan H Parks, Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J Mussig, Philip Hugenholtz. Nat Biotechnol 2020
350
6

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

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
6

MrBayes 3: Bayesian phylogenetic inference under mixed models.
Fredrik Ronquist, John P Huelsenbeck. Bioinformatics 2003
6


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
5

Quartet inference from SNP data under the coalescent model.
Julia Chifman, Laura Kubatko. Bioinformatics 2014
476
5

jModelTest 2: more models, new heuristics and parallel computing.
Diego Darriba, Guillermo L Taboada, Ramón Doallo, David Posada. Nat Methods 2012
5


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

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
5

Prokka: rapid prokaryotic genome annotation.
Torsten Seemann. 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


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

Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.
Per Erixon, Bodil Svennblad, Tom Britton, Bengt Oxelman. Syst Biol 2003
300
4

Relaxed phylogenetics and dating with confidence.
Alexei J Drummond, Simon Y W Ho, Matthew J Phillips, Andrew Rambaut. PLoS Biol 2006
4

Shifting the genomic gold standard for the prokaryotic species definition.
Michael Richter, Ramon Rosselló-Móra. Proc Natl Acad Sci U S A 2009
4

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
4

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
4

Animal mitochondrial genomes.
J L Boore. Nucleic Acids Res 1999
4


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

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
4

RDP4: Detection and analysis of recombination patterns in virus genomes.
Darren P Martin, Ben Murrell, Michael Golden, Arjun Khoosal, Brejnev Muhire. Virus Evol 2015
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.