Tree Viewer Broadcasting

To get more information about broadcasting please see the Broadcasting tutorial.

Introduction

Broadcasting is supported between two phylogenetic tree view if both trees have some node properties (attributes) and their values in common. Clicking on nodes or selecting groups of nodes in one tree will result in matching nodes, such as nodes with matching sequence ids, being highlighted in the other tree. You may want to compare tree topologies using the broadcast option in cases where you have trees created based on a partially similar set of the sequences. Additionally, you may want to use the broadcast option when two trees have same set of sequences but were created using different tree construction methods or were created by the same tree construction program but based on multiple alignments made using different alignment programs.

An example project can be downloaded from out ftp site.

Broadcasting by node selection

To see broadcasting (selection in both trees) you need to open two trees in the Tree View, place them side-by-side and click on a terminal node or branch node. The screenshot below shows how manual selection in one view reflects automatic broadcast selection in another view. In our example the trees have different topologies but were created based on the same set of sequences with the same ids. By default, the sequence id (seq-id) node property is used for broadcasting.

You can open trees in different layouts. The screenshot below shows the same trees in the Radial layout communicateing with each other via node selection.

Broadcasting by search queries

Another interesting example of broadcasting in the Tree View is using queries. Enter the query: “Thiobacillus” and check the box "All" in the first view. As you can see on the screenshot below the two terminal nodes get selected and broadcasted in the second view. Note: you can use any node attributes that are present in your tree for search. Attributes can be seen in the tooltips.

Broadcasting works through seq-id matching, but NOT by following the search query criteria (organism in our screenshot). In other words, search finds the node with the query organism in the first tree and then matches its seq-id to the corresponding seq-ids in another tree.

Properties (Attributes) for broadcasting

To broadcast selections between trees based on properties other than seq-id, you need to configure the property for broadcasting between trees using the Broadcast Options dialog/BioTree Settings Tab. To open it, please select Tools/Broadcast options or click the broadcast dialog icon on the upper panel:

In the Broadcast Options dialog open BioTree Settings tab:

You can select a property (by clicking on it) and perform certain operations:

• Edit a property after clicking the a|e button
• Add a new property by clicking the New item button and typing the new property name (for example host or country)
• Delete a property by clicking the Red cross button
• Move a property up and down in the priorities list by clicking the Up or Down Arrows

When broadcasting is enabled, selection is based on the first property in the list that is present in both trees. In the above examples, that property was seq-id. To update the list, use the icons on the right to add, change, delete or reorder the properties. These updates will apply to all tree broadcasting and will be saved between sessions. If the trees do not share any properties in the list, no broadcast selections will occur. Changing these properties will not affect broadcasting between trees and other non-tree views, such as the graphical view.

In our trees, there are some nodes which have the property “country”. Let’s add this property to the list, move it up to the first position, and click OK. Now broadcasting will work only for the nodes with the property “country”. As shown in the screenshot below, if you select an internal branch in one tree and that branch includes terminal nodes (leaves) with the property “country”, only these nodes will be broadcasted in the other tree.

In case trees you work with have different sets of properties, the first common property in the priority list will be used for broadcasting. the table below demonstrates the example where the first common property (attribute) for both trees is tax-id, and thus it will be used for broadcasting.