TreeDyn: towards dynamic graphics and annotations for analyses of trees
By François Chevenet, Marie-Christine Brun, Anne-Laure Bañuls, Bernard Jacq, Richard Christen. BMC Bioinformatics, 2006
1,075 citations recorded by the source corpus.
BackgroundAnalyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees.ResultsWe have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.ConclusionTreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections.
Subfields: Computer Vision and Pattern Recognition, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/fa8eaed21e0ff6cba18c8661d422c3be83880909
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Citations in the corpus
- ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data (2017, methodology): “Only a subset, such as FIGTREE , TREEDYN and ITOL , allows users to annotate trees with colouring branches, highlighted clades and tree features.”
- The Leptosphaeria maculans-Leptosphaeria biglobosa species complex in the American continent. (2009, methodology): “Plant Pathology (2009) 58, 1044–1058 using the TreeView and TreeDyn software (Chevenet et al., 2006; Page, 1996).”
- ETE: a python Environment for Tree Exploration (2010, neutral): “An intermediate alternative between standalone viewers and programmatic tree rendering is that of the TreeDyn program [14], which has support for some scripting options and can be used to create fully annotated tree images.”
- The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. (2009, methodology): “Character states were also mapped using the tree viewing program TreeDyn (Chevenet et al. 2006), shown in Figure 5.”
- Using ggtree to Visualize Data on Tree‐Like Structures (2020, methodology): “There are many software packages 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…”
- Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy (2011, background): “Tools like TREEVIEW (2), Archaeopteryx (3), TreeDyn (4), Dendroscope (5), PhyloWidget (6) and others provide many useful features and are used regularly by scientists worldwide.”
- TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses (2010, methodology): “To date, a variety of tree visualization tools have been released, among which ATV [17], Dendroscope [18], FigTree (the tree editor accompanying BEAST), the MEGA tree explorer [19], Mesquite [20], PhyloWidget [21], TreeDyn [22] and TreeView [23] may be the most widely distributed.”
- Astrosphaeriella is polyphyletic, with species in Fissuroma gen. nov., and Neoastrosphaeriella gen. nov. (2011, methodology): “1 by using graphical options available in TreeDyn v. 198.3 (Chevenet et al. 2006).”
- BLAST-EXPLORER helps you building datasets for phylogenetic analysis (2010, methodology): “The tree is generated by combining ClustalW [6] and TreeDyn [7] using either all sites of the BLAST-reconstructed multiple-alignment or gap-free sites only (N.B., the initial tree is computed using all sites). o The “ Add sequences to tree ” option allow incorporating up to five external sequences…”
- The genome of Theobroma cacao (2011, neutral): “Cacao chromosome Arabidopsis chromosome C1(1321) A1(63)-A2(85)-A3(69)-A4(116)-A5(64) C2(935) A1(89)-A2(30)-A4(61)-A5(10) C3(1018) A1(70)-A3(17)-A4(63)-A5(130) C4(837) A1(21)-A2(9)-A3(94)-A4(36)-A5(44) C5(820) A1(24)-A2(51)-A3(78)-A5(37) C6(616) A1(59)-A2(15)-A4(66)-A5(26) C7(287) A1(5)-A5(32) C8(605”
- Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “The resultant plasmid has the”