A citation-based method for searching scientific literature


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



Times Cited
  Times     Co-cited
Similarity



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
32


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
27

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
26


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
19

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
17

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
17

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

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Felipe A Simão, Robert M Waterhouse, Panagiotis Ioannidis, Evgenia V Kriventseva, Evgeny M Zdobnov. Bioinformatics 2015
14

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
13

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
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
648
12

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
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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
10

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman. Genome Biol 2008
10


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
10

Animal mitochondrial genomes.
J L Boore. Nucleic Acids Res 1999
10

MEGA11: Molecular Evolutionary Genetics Analysis Version 11.
Koichiro Tamura, Glen Stecher, Sudhir Kumar. Mol Biol Evol 2021
857
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
9

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng,[...]. Nat Biotechnol 2011
9

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
9

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Bruce J Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K Young,[...]. PLoS One 2014
9




NOVOPlasty: de novo assembly of organelle genomes from whole genome data.
Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits. Nucleic Acids Res 2017
8

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
W H Majoros, M Pertea, S L Salzberg. Bioinformatics 2004
767
8



Gene finding in novel genomes.
Ian Korf. BMC Bioinformatics 2004
8

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
8

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
7


Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.
Joshua N Burton, Andrew Adey, Rupali P Patwardhan, Ruolan Qiu, Jacob O Kitzman, Jay Shendure. Nat Biotechnol 2013
659
7

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

CAFE: a computational tool for the study of gene family evolution.
Tijl De Bie, Nello Cristianini, Jeffery P Demuth, Matthew W Hahn. Bioinformatics 2006
797
7

MrBayes 3: Bayesian phylogenetic inference under mixed models.
Fredrik Ronquist, John P Huelsenbeck. Bioinformatics 2003
7

Ultrafast approximation for phylogenetic bootstrap.
Bui Quang Minh, Minh Anh Thi Nguyen, Arndt von Haeseler. Mol Biol Evol 2013
7

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

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.
Kazutaka Katoh, John Rozewicki, Kazunori D Yamada. Brief Bioinform 2019
6

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
6

Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.
Mira V Han, Gregg W C Thomas, Jose Lugo-Martinez, Matthew W Hahn. Mol Biol Evol 2013
380
6

GeneWise and Genomewise.
Ewan Birney, Michele Clamp, Richard Durbin. Genome Res 2004
6


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.