A citation-based method for searching scientific literature

Dong Zhang, Fangluan Gao, Ivan Jakovlić, Hong Zou, Jin Zhang, Wen X Li, Gui T Wang. Mol Ecol Resour 2020
Times Cited: 558







List of co-cited articles
371 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
51


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
43

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
35

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
Sudhir Kumar, Glen Stecher, Koichiro Tamura. Mol Biol Evol 2016
25

Ultrafast approximation for phylogenetic bootstrap.
Bui Quang Minh, Minh Anh Thi Nguyen, Arndt von Haeseler. Mol Biol Evol 2013
19

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
18

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
17

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
17

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
16

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
16



Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard. Syst Biol 2018
12

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
12

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang, Yu Song, Claude W dePamphilis, Ting-Shuang Yi, De-Zhu Li. Genome Biol 2020
554
12


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
10

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
10

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

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes.
Xiao-Jian Qu, Michael J Moore, De-Zhu Li, Ting-Shuang Yi. Plant Methods 2019
358
9

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


NOVOPlasty: de novo assembly of organelle genomes from whole genome data.
Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits. Nucleic Acids Res 2017
9

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


REPuter: the manifold applications of repeat analysis on a genomic scale.
S Kurtz, J V Choudhuri, E Ohlebusch, C Schleiermacher, J Stoye, R Giegerich. Nucleic Acids Res 2001
893
8

Animal mitochondrial DNA: structure and evolution.
D R Wolstenholme. Int Rev Cytol 1992
8


GeSeq - versatile and accurate annotation of organelle genomes.
Michael Tillich, Pascal Lehwark, Tommaso Pellizzer, Elena S Ulbricht-Jones, Axel Fischer, Ralph Bock, Stephan Greiner. Nucleic Acids Res 2017
989
8


IRscope: an online program to visualize the junction sites of chloroplast genomes.
Ali Amiryousefi, Jaakko Hyvönen, Peter Poczai. Bioinformatics 2018
194
8

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

Bandage: interactive visualization of de novo genome assemblies.
Ryan R Wick, Mark B Schultz, Justin Zobel, Kathryn E Holt. Bioinformatics 2015
735
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

Chloroplast genomes: diversity, evolution, and applications in genetic engineering.
Henry Daniell, Choun-Sea Lin, Ming Yu, Wan-Jung Chang. Genome Biol 2016
448
7

Animal mitochondrial genomes.
J L Boore. Nucleic Acids Res 1999
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
6

MISA-web: a web server for microsatellite prediction.
Sebastian Beier, Thomas Thiel, Thomas Münch, Uwe Scholz, Martin Mascher. Bioinformatics 2017
458
6

MRBAYES: Bayesian inference of phylogenetic trees.
J P Huelsenbeck, F Ronquist. Bioinformatics 2001
6




VISTA: computational tools for comparative genomics.
Kelly A Frazer, Lior Pachter, Alexander Poliakov, Edward M Rubin, Inna Dubchak. Nucleic Acids Res 2004
6



The CGView Server: a comparative genomics tool for circular genomes.
Jason R Grant, Paul Stothard. Nucleic Acids Res 2008
662
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.