Tree viewing software is used to visualize phylogenetic trees, which show evolutionary relationships. There are both free and commercial tree visualization programs available. TreeView and TreeViewX are examples of free, open-source software that can read various file formats and display, edit, and export phylogenetic trees. TreeViewJ is also open-source and allows users to annotate, edit, and produce publication-ready phylogenetic tree figures. It has a graphical user interface with options to visualize sample collection dates on a timeline.

1. TREE VIEWING
SOFTWARE
Jayakrishnan KG
MSc.Bioinformatics

2. ◦ Phylogenetic tree viewing software is a compilation of software tools
and web portals used in visualizing phylogenetic trees.
◦ Phylogenetic trees are widely used to visualize evolutionary
relationships between different organisms or samples of the same
organism.
◦ There are a variety of both free and commercial tree visualization
software available.

3. TreeView
◦ TreeView is a program to view phylogenetic trees in your computer. A
phylogenetic tree is a graphical representation of a hypothesis about the
evolution of a species, with branches that separate, hybridize, or become
terminated by extinction.
◦ TreeView can read and display some of the most used tree file formats, such as
NEXUS, PHYLIP, Hennig86, NONA, MEGA, and ClustalW/X.
◦ Once loaded in the application, you can choose to view the tree as a Radial
Tree, a Cladogram (or a Rectangular Cladogram) or a Phylogram.
◦ You can edit the trees using the built-in Tree Editor, which will let you move,
collapse or expand branches, reroot trees, rotate or swap descendants, and
apply labels.

5. ◦ You can export any loaded tree to the NEXUS, PHYLIP, or Hennig86
formats, as well as a graphic file, in either .EMF or .WMF format. You can
also print any tree. It is possible to print multiple trees in a single page and
one tree over more than one page.

7. TreeView X
◦ TreeView X is an open source and multi-platform program to display phylogenetic
trees.
◦ It can read and display NEXUS and Newick format tree files (such as those output by
PAUP*, ClustalX, TREE-PUZZLE, and other programs). It allows users to order the
branches of the trees, and to export the trees in SVG(Scalable Vector Graphics)
format.
◦ TreeView X is written in C++.
◦ The most striking feature of Tree View is its user interface, which is extremely user
friendly and designed especially for the Windows operating system.

8. ◦ Features include:
◦ Tree editor:
◦ Slanted cladogram.
◦ Rectangular cladogram.
◦ Phylogram.
◦ Drag-and-drop.
o Show internal node labels.
◦ Zoom.
◦ Reads many different tree file formats (including NEXUS, PHYLIP, Hennig86, NONA, MEGA, and
ClustalW/X).
◦ Support for picture files (SVG and EMF).
◦ Export to SVG format.
◦ Print preview.
◦ Print multiple trees per page, and one tree over more than one page.

10. ◦ There are some drawbacks to Treeview X :
◦ There is a slight delay in the loading of the page when the entire
window is displayed.
◦ The display of thumbnails sometimes doesn't change or fit with the
rest of the page.

11. TreeView J
◦ TreeViewJ is a visualization program which will allow researchers to
annotate, edit and produce publication-ready figures of phylogenetic
trees, and to visualize sample collection date information using a
timeline.
◦ TreeViewJ is written in Java.
◦ A variety of file formats exist for the storage of phylogenetic trees. Some
of them are:
◦ New Hampshire - format which store only the node name and branch length information.
◦ New Hampshire Extended and Nexus - formats, can be used to store other data such as
formatting and sequence data.
◦ Lucid and Structure of Descriptive Data (SDD) - formats have been used for the
description of taxonomic data.

12. Graphical User Interface
◦ The main user interface for TreeViewJ, 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.

13. 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.

14. ◦ TreeViewJ can represent phylogenies as slanted cladograms, rectangular
cladograms, circular cladograms, and phylograms.

15. ◦ Once a tree is drawn the user can zoom in and out, change the draw
color, and toggle internal and leaf labels on and off. Zooming and resizing
are achieved using affine transforms to avoid redraws.
◦ The editor allows changes to be made to node name and font color, as
well as the branch width and color.
◦ Nodes of the tree can be selected by right clicking or clicking and
dragging and their labels may be copied to the clipboard and pasted into
other applications.
◦ Once the tree is drawn, it can be printed or exported to either Scalable
Vector Graphics (SVG) or JPEG format.

16. ◦ It is the first tree viewer to include support for
date mapping and sorting.
◦ Leaf nodes are assigned the dates of the
samples they represent.
◦ Here, it is being used to sort the taxa
alphabetically. The numbers above the internal
nodes show the order that sorting is done in.
◦ 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.

17. Thank You