A citation-based method for searching scientific literature

Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab. BMC Bioinformatics 2018
Times Cited: 388







List of co-cited articles
809 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
46


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
33

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
31

UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Le Sy Vinh. Mol Biol Evol 2018
27

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
24


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
20

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
19

ASTRAL: genome-scale coalescent-based species tree estimation.
S Mirarab, R Reaz, Md S Bayzid, T Zimmermann, M S Swenson, T Warnow. Bioinformatics 2014
483
19

Quartet inference from SNP data under the coalescent model.
Julia Chifman, Laura Kubatko. Bioinformatics 2014
385
19


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

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.
Brant C Faircloth, John E McCormack, Nicholas G Crawford, Michael G Harvey, Robb T Brumfield, Travis C Glenn. Syst Biol 2012
479
16

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
16

New Methods to Calculate Concordance Factors for Phylogenomic Datasets.
Bui Quang Minh, Matthew W Hahn, Robert Lanfear. Mol Biol Evol 2020
68
23

Whole-genome analyses resolve early branches in the tree of life of modern birds.
Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard,[...]. Science 2014
835
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
15



BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.
Robert M Waterhouse, Mathieu Seppey, Felipe A Simão, Mosè Manni, Panagiotis Ioannidis, Guennadi Klioutchnikov, Evgenia V Kriventseva, Evgeny M Zdobnov. Mol Biol Evol 2018
825
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
723
13

BEAST 2: a software platform for Bayesian evolutionary analysis.
Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A Suchard, Andrew Rambaut, Alexei J Drummond. PLoS Comput Biol 2014
13

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
13

Gene tree discordance, phylogenetic inference and the multispecies coalescent.
James H Degnan, Noah A Rosenberg. Trends Ecol Evol 2009
817
13



phangorn: phylogenetic analysis in R.
Klaus Peter Schliep. Bioinformatics 2011
12

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Alexey M Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, Alexandros Stamatakis. Bioinformatics 2019
500
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
11

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
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


De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Brian J Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,[...]. Nat Protoc 2013
10

Discordance of species trees with their most likely gene trees.
James H Degnan, Noah A Rosenberg. PLoS Genet 2006
479
9

APE: Analyses of Phylogenetics and Evolution in R language.
Emmanuel Paradis, Julien Claude, Korbinian Strimmer. Bioinformatics 2004
9

Resolving difficult phylogenetic questions: why more sequences are not enough.
Hervé Philippe, Henner Brinkmann, Dennis V Lavrov, D Timothy J Littlewood, Michael Manuel, Gert Wörheide, Denis Baurain. PLoS Biol 2011
553
9

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life.
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R. Nat Ecol Evol 2017
104
9




The variant call format and VCFtools.
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry,[...]. Bioinformatics 2011
9


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

Anchored hybrid enrichment for massively high-throughput phylogenomics.
Alan R Lemmon, Sandra A Emme, Emily Moriarty Lemmon. Syst Biol 2012
337
8


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.