Bioinformatics Toolbox

Tools Menu

Inspect Mode Command

Use the inspect mode to compare path distances between sequences and to search for related sequences that might not be physically drawn close together.

1. From the Tools menu, click Inspect, or from the toolbar, click the Inspect Tool mode icon .

   The Phylogenetic Tree Tool is set to inspect mode.

2. Point to a branch or leaf node.

   A pop-up window opens with information about the patristic distances to parent and root nodes.

   

3. Click a branch or leaf node, and then move your mouse over another leaf node.

   The tool highlights the path between nodes and displays the path length in the pop-up window . The path length is the patristic distances calculated by seqlinkage.

   

Collapse/Expand Branch Mode Command

Some trees can have thousands of leaf and branch nodes. Displaying all the nodes can create a tree diagram that is unreadable. By collapsing some of the branches, you can better see the relationships between the remaining nodes.

1. From the Tools menu, click Collapse/Expand, or from the toolbar, click the Collapse/Expand node icon .

   The Phylogenetic Tree Tool is set to collapse/expand mode.

2. Point to a branch.

   The selected paths to collapse (remove from view) are highlighted in gray.

   

3. Click the branch node.

   The tool removes the display of branch and leaf nodes below the selected branch. The data is not removed.

   

4. To expand a branch, point to a collapsed branch and click.

Rotate Branch Mode Command

A phylogenetic tree is initially created by pairing the two most similar sequences and then adding the remaining sequences in a decreasing order of similarity. You might want to rotate branches to emphasize the direction of evolution.

1. From the Tools menu, click Rotate Branch, or from the toolbar, click the Rotate Branch mode icon .

   The Phylogenetic Tree Tool is set to rotate branch mode.

2. Point to a branch node.

   

3. Click the branch node.

   

   The branch and leaf nodes are rotated 180 degrees around the selected branch node.

Rename Leaf/Branch Mode Command

The Phylogenetic Tree Tool takes the node names from the phytree object and creates numbered branch names starting with Branch 1. You can edit and change or replace any of the leaf or branch names. Changes to branch and leaf names are saved when you use the Save command.

1. From the Tools menu, click Rename, or from the toolbar, click the Rename mode icon .

2. Click a branch or leaf node.

   

   A text box opens with the current name of the node.

3. In the text box, edit or enter an new name.

   

4. To save your changes, click outside of text box.

Prune (delete) Leaf/Branch Mode Command

Your tree might contain leaves that are far outside the phylogeny, or it might have duplicate leaves that you want to remove.

1. From the Tools menu, click Prune, or from the toolbar, click the prune icon .

   The Phylogenetic Tree Tool is set to rename mode.

2. Point to a branch or leaf node.

   

   For leaf node, the branch line connected to the leaf is highlighted in gray. For a branch nodes, the branch lines below the node are highlighted in light gray.

   Note   If you delete nodes (branches or leaves), you cannot undo the changes. The Phylogenetic Tree Tool does not have an Undo command.

3. Click the branch or leaf node.

   The branch is removed from the figure and the other nodes are rearranged to balance the tree structure. The phylogeny is not recalculated.

Zoom In, Zoom Out, and Pan Commands

The Zoom and Pan commands are the standard controls with MATLAB figures for resizing and moving the screen.

1. From the Tools menu, click Zoom In, or from the toolbar click the zoom in icon .

   The tool activates zoom n mode and changes the cursor to a magnifying glass.

   

2. Place the cursor over the section of the tree diagram you want to enlarge and then click.

   The tree diagram is enlarged to twice its size.

   

3. From the toolbar click the Pan icon .

4. Move the cursor over the tree diagram, left-click, and drag the diagram to the location you want to view.

Zoom In , Zoom Out , Pan

Threshold Collapse Command

Use the Threshold Collapse command to collapse the display of nodes using a distance criterion instead of interactively selecting nodes with the Collapse/Expand command. Branches with distances below the threshold are collapsed from the display.

1. From the Tools menu, click Threshold Collapse, and select one of the following:

   • Distance to Leaves — Sets the threshold starting from the right of the tree.

   • Distance to Root — Sets the threshold starting from the root node at the left side of the tree.

   The collapse slider bar is displayed at the top of the diagram.

   

2. Click and drag the slider bar to the left to set the distance threshold.

   

3. Click the OK button to the right of the slider. The nodes below the distance threshold are hidden.

   

Expand All Command

The data for branches and leaves you hide with the Collapse/Expand or Threshold Collapse commands is not removed from the tree. You can display the hidden data using these commands or display all hidden data with the Expand All command.

1. From the Tool menu, click Expand All. The hidden branches and leaves are displayed.

   

Find Leaf/Branch Command

Phylogenetic trees can have thousands of leaves and branches, and finding a specific node can be difficult. Use the Find command to locate a node using its name or part of its name.

1. From the Tools menu, click Find Leaf/Branch.

   The Find Leaf/Branch dialog opens.

   

2. In the Regular Expression to match box, enter a name or partial name of a branch or leaf.

3. Click OK.

Fit to Window

After you hide nodes with the Collapse/Expand or Threshold Collapse commands, or delete nodes with the Prune command, there might be extra space in the tree diagram. Use the Fit to Window command to redraw the tree diagram to fill the entire figure window.

1. From the Tools menu, click Fit to Window.

Reset View Command

Use the Reset Window command to remove formatting changes such as rotations, collapsed branches, and zooms.

1. From the Tools menu, click Reset Window.

Options Submenu

Use the Options command to select the behavior for the zoom and pan modes.

• Unconstrained Zoom — Allow zooming in both horizontal and vertical directions.

• Horizontal Zoom — Restrict zoom to the horizontal direction.

• Vertical Zoom — Zoom only in the vertical direction (default).

• Unconstrained Pan — Allow panning in both horizontal and vertical directions.

• Horizontal Pan — Restrict panning to horizontal direction.

• Vertical Pan — Pan only in the vertical direction (default).

File Menu

Windows Menu

© 1994-2005 The MathWorks, Inc.