Cargando…
TreeDyn: towards dynamic graphics and annotations for analyses of trees
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...
Autores principales: | , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2006
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1615880/ https://www.ncbi.nlm.nih.gov/pubmed/17032440 http://dx.doi.org/10.1186/1471-2105-7-439 |
_version_ | 1782130492356689920 |
---|---|
author | Chevenet, François Brun, Christine Bañuls, Anne-Laure Jacq, Bernard Christen, Richard |
author_facet | Chevenet, François Brun, Christine Bañuls, Anne-Laure Jacq, Bernard Christen, Richard |
author_sort | Chevenet, François |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-1615880 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-16158802006-10-18 TreeDyn: towards dynamic graphics and annotations for analyses of trees Chevenet, François Brun, Christine Bañuls, Anne-Laure Jacq, Bernard Christen, Richard BMC Bioinformatics Software 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. BioMed Central 2006-10-10 /pmc/articles/PMC1615880/ /pubmed/17032440 http://dx.doi.org/10.1186/1471-2105-7-439 Text en Copyright © 2006 Chevenet et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Chevenet, François Brun, Christine Bañuls, Anne-Laure Jacq, Bernard Christen, Richard TreeDyn: towards dynamic graphics and annotations for analyses of trees |
title | TreeDyn: towards dynamic graphics and annotations for analyses of trees |
title_full | TreeDyn: towards dynamic graphics and annotations for analyses of trees |
title_fullStr | TreeDyn: towards dynamic graphics and annotations for analyses of trees |
title_full_unstemmed | TreeDyn: towards dynamic graphics and annotations for analyses of trees |
title_short | TreeDyn: towards dynamic graphics and annotations for analyses of trees |
title_sort | treedyn: towards dynamic graphics and annotations for analyses of trees |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1615880/ https://www.ncbi.nlm.nih.gov/pubmed/17032440 http://dx.doi.org/10.1186/1471-2105-7-439 |
work_keys_str_mv | AT chevenetfrancois treedyntowardsdynamicgraphicsandannotationsforanalysesoftrees AT brunchristine treedyntowardsdynamicgraphicsandannotationsforanalysesoftrees AT banulsannelaure treedyntowardsdynamicgraphicsandannotationsforanalysesoftrees AT jacqbernard treedyntowardsdynamicgraphicsandannotationsforanalysesoftrees AT christenrichard treedyntowardsdynamicgraphicsandannotationsforanalysesoftrees |