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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

Tree Sorting in TreeViewJ. The sorting algorithm used in TreeViewJ. Here, it is being used to sort the taxa alphabetically. The numbers above the internal nodes show the order that sorting is done in.
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Figure 2: Tree Sorting in TreeViewJ. The sorting algorithm used in TreeViewJ. Here, it is being used to sort the taxa alphabetically. The numbers above the internal nodes show the order that sorting is done in.

Mentions: Phylogenic trees are sorted by date in the most straightforward way possible: a depth-first post-order sort of the children at each node. Leaf nodes are assigned the dates of the samples they represent. Internal nodes are assigned the minimum (ascending) or maximum (descending) date of its children. The resulting tree is isomorphic to the original tree, with the taxa sorted in ascending (oldest samples on top) or descending (youngest on top) order (Figure 2).


TreeViewJ: An application for viewing and analyzing phylogenetic trees.

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

Tree Sorting in TreeViewJ. The sorting algorithm used in TreeViewJ. Here, it is being used to sort the taxa alphabetically. The numbers above the internal nodes show the order that sorting is done in.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Tree Sorting in TreeViewJ. The sorting algorithm used in TreeViewJ. Here, it is being used to sort the taxa alphabetically. The numbers above the internal nodes show the order that sorting is done in.
Mentions: Phylogenic trees are sorted by date in the most straightforward way possible: a depth-first post-order sort of the children at each node. Leaf nodes are assigned the dates of the samples they represent. Internal nodes are assigned the minimum (ascending) or maximum (descending) date of its children. The resulting tree is isomorphic to the original tree, with the taxa sorted in ascending (oldest samples on top) or descending (youngest on top) order (Figure 2).

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