Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

By Daniel H. Huson, Céline Scornavacca. Systematic Biology, 2012

1,606 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/7372f488efdd2e49edbb32bb38e4807c3108eec5

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

1. M. Lavin
2. M. Wojciechowski
3. R. Pennington
4. J. Doyle
5. C. Hughes
6. Anne Bruneau
7. M. Simon
8. P. Herendeen

Citations in the corpus

• ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data (2017, methodology): “There are many software packages and Web tools that are designed for displaying phylogenetic trees, such as TREEVIEW (Page 1996), FIGTREE (Rambaut 2014), TREEDYN (Chevenet et al. 2006), ITOL (Letu-nic & Bork 2011), EVOLVIEW (Zhang et al. 2012) and DENDRO-SCOPE (Huson & Scornavacca 2012).”
• Inferring Phylogenetic Networks Using PhyloNet (2017, methodology): “Phylogenetic networks inferred by PhyloNet are represented using an extended Newick format and can be readily visualized by Dendroscope (Huson and Scornavacca, 2012).”
• Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021, background): “Nowadays, various software packages offer additional tree annotation features, both online and as stand-alone packages or libraries, for example ETE toolkit (4), ggtree (5), Dendroscope (6), PhyD3 (7) or Evolview (8).”
• Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, background): “Dendroscope This supports envision of bulky trees and offers numerous choices to trace the sketching through a command line (Huson & Scornavacca 2012).”
• GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens (2017, unknown): “Dendrograms generated by other programs (FigTree [v.1.4.3, http://tree.bio.ed.ac.uk/software/figtree/]; Dendroscope [Huson and Scornavacca 2012]) from large data sets were also difficult to interpret.”
• PhyloNetworks: A Package for Phylogenetic Networks (2017, methodology): “Other software packages can estimate phylogenetic networks (notably PhyloNet [Than et al. 2008], BEAST2 [Zhang et al. 2017], and TreeMix [Pickrell and Pritchard 2012]) or plot rooted networks (Dendroscope, Huson and Scornavacca, 2012).”
• Using ggtree to Visualize Data on Tree‐Like Structures (2020, unknown): “…and web tools that are designed for displaying phylogenetic trees, such as TreeView (Page, 2003), FigTree, TreeDyn (Chevenet, Brun, Bañuls, Jacq, & Christen, 2006), Dendroscope (Huson & Scornavacca, 2012), EvolView (Subramanian, Gao, Lercher, Hu, & Chen, 2019), and iTOL (Letunic & Bork, 2007).”
• A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny (2017, background): “However, there is no uncertainty surrounding the paraphyly of subfamily Version of Record TAXON 66 (1) • February 2017: 44–77 LPWG • Phylogeny and classification of the Leguminosae [http://dendroscope.org/]; Huson & Scornavacca, 2012), and downloaded from Supplementary Data: Data file B.”
• BUSCO: Assessing Genomic Data Quality and Beyond (2021, methodology): “To visualize the Newick file, you can use any program for viewing phylogenetic trees, e.g., Dendroscope (Huson & Scornavacca, 2012).”
• Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019, background): “Nowadays, various other software packages offer additional tree annotation features, both online and as standalone packages, for example ETE toolkit (6), Dendroscope (7) or Evolview (8).”
• ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016, methodology): “Although several software packages are available for the standalone exploration of trees (Letunic and Bork 2007; Huson and Scornavacca 2012; Asnicar et al. 2015) and the programmatic manipulation of data (Paradis et al. 2004; Knight et al. 2007; Sukumaran and Holder 2010; Vos et al. 2011; Talevich…”