Phylogenetic Tree viewing softwares
- 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