TreeDyn: towards dynamic graphics and annotations for analyses of treesReport as inadecuate




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* Corresponding author 1 GEMI - Génétique et évolution des maladies infectieuses 2 IBDM - Institut de Biologie du Développement de Marseille 3 ISBDC - Institut de signalisation, biologie du développement et cancer

Abstract : BACKGROUND: Analyses 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.RESULTS: We 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.CONCLUSION: TreeDyn 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.





Author: François Chevenet - Christine Brun - Anne-Laure Bañuls - Bernard Jacq - Richard Christen -

Source: https://hal.archives-ouvertes.fr/



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