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TreeViewJ: An application for viewing and analyzing phylogenetic trees.

Peterson MW, Colosimo ME - Source Code Biol Med (2007)

Bottom Line: We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees.If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees.

View Article: PubMed Central - HTML - PubMed

Affiliation: The MITRE Corporation, 202 Burlington Rd, Bedford, MA, USA. mcolosimo@mitre.org.

ABSTRACT

Background: Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images.

Results: We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.

Conclusion: TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net.

No MeSH data available.


Related in: MedlinePlus

TreeViewJ User Interface. The main user interface for TreeViewJ. Multiple files, one of which contains multiple trees, are open. The currently displayed tree contains colored taxon names, and has had its taxa mapped to a timeline.
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Figure 1: TreeViewJ User Interface. The main user interface for TreeViewJ. Multiple files, one of which contains multiple trees, are open. The currently displayed tree contains colored taxon names, and has had its taxa mapped to a timeline.

Mentions: The main user interface for TreeViewJ, shown in Figure 1, is composed of two panels. The left panel displays open files (referred to as "forests") and the trees stored within them. Tooltips are used to display a description of the tree, if one exists. The user can move trees between files by either copying and pasting, or using drag and drop. Trees may also be deleted from forests. Visualization and editing options are easily accessible via menus and toolbars. The right panel contains a scroll pane which displays the currently selected tree.


TreeViewJ: An application for viewing and analyzing phylogenetic trees.

Peterson MW, Colosimo ME - Source Code Biol Med (2007)

TreeViewJ User Interface. The main user interface for TreeViewJ. Multiple files, one of which contains multiple trees, are open. The currently displayed tree contains colored taxon names, and has had its taxa mapped to a timeline.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2170439&req=5

Figure 1: TreeViewJ User Interface. The main user interface for TreeViewJ. Multiple files, one of which contains multiple trees, are open. The currently displayed tree contains colored taxon names, and has had its taxa mapped to a timeline.
Mentions: The main user interface for TreeViewJ, shown in Figure 1, is composed of two panels. The left panel displays open files (referred to as "forests") and the trees stored within them. Tooltips are used to display a description of the tree, if one exists. The user can move trees between files by either copying and pasting, or using drag and drop. Trees may also be deleted from forests. Visualization and editing options are easily accessible via menus and toolbars. The right panel contains a scroll pane which displays the currently selected tree.

Bottom Line: We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees.If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees.

View Article: PubMed Central - HTML - PubMed

Affiliation: The MITRE Corporation, 202 Burlington Rd, Bedford, MA, USA. mcolosimo@mitre.org.

ABSTRACT

Background: Phylogenetic trees are widely used to visualize evolutionary relationships between different organisms or samples of the same organism. There exists a variety of both free and commercial tree visualization software available, but limitations in these programs often require researchers to use multiple programs for analysis, annotation, and the production of publication-ready images.

Results: We present TreeViewJ, a Java tool for visualizing, editing and analyzing phylogenetic trees. The software allows researchers to color and change the width of branches that they wish to highlight, and add names to nodes. If collection dates are available for taxa, the software can map them onto a timeline, and sort the tree in ascending or descending date order.

Conclusion: TreeViewJ is a tool for researchers to visualize, edit, "decorate," and produce publication-ready images of phylogenetic trees. It is open-source, and released under an GPL license, and available at http://treeviewj.sourceforge.net.

No MeSH data available.


Related in: MedlinePlus