Tree Viewer Broadcasting

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

Introduction

Broadcasting is supported between phylogenetic tree views. This can be very useful for finding similarities or differences between two open trees. 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.

Step 1

Step 2

The project contains two trees, please open both of them using "Tree View" and place views side-by-side. For the second tree: 'get_snp_17_2_asn' use the context menu to change layout style to Circular.

Step 3

Click on a random node in one tree to see effect of broadcasting on the other Tree View. As data supporting both treee views are not equal please try selecting other nodes if you do not see the desiured effect.

Effect of broadcasting on another tree view

The screenshot above shows how manual selection in one view reflects in automatic broadcast selection in another view. Note that the partner view contains a different tree with very different topology, but the system knows what to select, in this case using the node attribute "seq-id" (sequence id). Tooltips on the screenshot display lists of available attributes.

Step 4

Another interesting example of broadcasting in Tree View is using queries. Enter the query: "dist >= 11" and check-box "All" in the first view to select more than one node.

Select more than one node

As you can see on the screenshot the multi-node selection gets broadcast and reflected in the second view. The second view topology is different and broadcasting works through seq-id matching, NOT by following the query criteria (distance).

Step 5

If you want to broadcast selections between trees based on attributes other than seq-id, then configure the attributes for broadcasting between trees using the phylogenetic tree "Properties" dialog. To open this dialog, right-click in one of the tree views and select "Settings…". When the dialog opens, select the "Broadcast Parameters" tab to show the below options.

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.

Properties dialog

You can select an attribute (by clicking on it) and perform certain operations:

  • Edit it after clicking a|e button
  • Delete it by clicking the delete (red cross) button
  • Move it up and down the prioritioes list by clicking the up or down arrows

You can also add attribute by clicking the New item button or just by clicking below the list.

New parameter

Tree-to-tree broadcasting example

To illustrate broadcasting based on the first property in the list that is present in both trees let us look at two trees, their attributes, and the current attributes list in the broadcastion priorities list in the properties menu.

   Tree 1 attributes       Tree 2 attributes       Broadcasting priorities list   
   seq-id    label    seq-id
   tax-id    asm-accession    asm-accession
   label    tax-id    tax-id
       label
In this example broadcasting will be based on tax-id because it is the first attribute in the priorities list that is present in both Tree 1 and Tree 2.

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Last updated: 2017-11-04T03:25:26Z