Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
Times Cited: 10328
Times Cited: 10328
Times Cited
Times Co-cited
Similarity
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
N Saitou, M Nei. Mol Biol Evol 1987
N Saitou, M Nei. Mol Biol Evol 1987
12
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
J D Thompson, D G Higgins, T J Gibson. Nucleic Acids Res 1994
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CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP.
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MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
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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
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Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies.
Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun. Int J Syst Evol Microbiol 2017
Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon, Jeongmin Lim, Yeseul Kim, Hyungseok Seo, Jongsik Chun. Int J Syst Evol Microbiol 2017
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Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
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Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
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MEME SUITE: tools for motif discovery and searching.
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
Timothy L Bailey, Mikael Boden, Fabian A Buske, Martin Frith, Charles E Grant, Luca Clementi, Jingyuan Ren, Wilfred W Li, William S Noble. Nucleic Acids Res 2009
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The variant call format and VCFtools.
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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
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Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
K Tamura, M Nei. Mol Biol Evol 1993
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5
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk, Markus Göker. BMC Bioinformatics 2013
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Evolutionary trees from DNA sequences: a maximum likelihood approach.
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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.
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The Pfam protein families database in 2019.
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Clustal W and Clustal X version 2.0.
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Molecular Evolutionary Genetics Analysis (MEGA) for macOS.
Glen Stecher, Koichiro Tamura, Sudhir Kumar. Mol Biol Evol 2020
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4
The EMBL-EBI search and sequence analysis tools APIs in 2019.
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Circos: an information aesthetic for comparative genomics.
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PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
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4
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
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4
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
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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
3
PLINK: a tool set for whole-genome association and population-based linkage analyses.
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3
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Heng Li, Richard Durbin. Bioinformatics 2010
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3
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
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3
Primer3--new capabilities and interfaces.
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3
CDD/SPARCLE: the conserved domain database in 2020.
Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song,[...]. Nucleic Acids Res 2020
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3
SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
3
Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases.
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3
DNA barcoding Australia's fish species.
Robert D Ward, Tyler S Zemlak, Bronwyn H Innes, Peter R Last, Paul D N Hebert. Philos Trans R Soc Lond B Biol Sci 2005
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TimeTree: A Resource for Timelines, Timetrees, and Divergence Times.
Sudhir Kumar, Glen Stecher, Michael Suleski, S Blair Hedges. Mol Biol Evol 2017
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SMART: recent updates, new developments and status in 2020.
Ivica Letunic, Supriya Khedkar, Peer Bork. Nucleic Acids Res 2021
Ivica Letunic, Supriya Khedkar, Peer Bork. Nucleic Acids Res 2021
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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
3
GSDS 2.0: an upgraded gene feature visualization server.
Bo Hu, Jinpu Jin, An-Yuan Guo, He Zhang, Jingchu Luo, Ge Gao. Bioinformatics 2015
Bo Hu, Jinpu Jin, An-Yuan Guo, He Zhang, Jingchu Luo, Ge Gao. Bioinformatics 2015
3
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
3
Prodigal: prokaryotic gene recognition and translation initiation site identification.
Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
3
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
Donovan H Parks, Michael Imelfort, Connor T Skennerton, Philip Hugenholtz, Gene W Tyson. Genome Res 2015
3
3
OrthoANI: An improved algorithm and software for calculating average nucleotide identity.
Imchang Lee, Yeong Ouk Kim, Sang-Cheol Park, Jongsik Chun. Int J Syst Evol Microbiol 2016
Imchang Lee, Yeong Ouk Kim, Sang-Cheol Park, Jongsik Chun. Int J Syst Evol Microbiol 2016
3
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
3
Shifting the genomic gold standard for the prokaryotic species definition.
Michael Richter, Ramon Rosselló-Móra. Proc Natl Acad Sci U S A 2009
Michael Richter, Ramon Rosselló-Móra. Proc Natl Acad Sci U S A 2009
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TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.
Jan P Meier-Kolthoff, Markus Göker. Nat Commun 2019
Jan P Meier-Kolthoff, Markus Göker. Nat Commun 2019
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Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens.
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Identification of group A rotavirus gene 4 types by polymerase chain reaction.
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2
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.