| Bioinformatics Toolbox | |
| The File menu includes the standard commands for opening and closing a file, and it includes commands to use phytree object data from the MATLAB workspace.The File menu commands are shown below. |
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Use the New Tool command to open tree data from a file into a second Phylogenetic Tree Tool window.
From the File menu, click New Tool.
The Select Phylogenetic Tree File dialog opens.
Select a directory and select a file with the extension .tree, and then click Open. The Bioinformatics Toolbox uses the file extension .tree for Newick formatted files, but you can use any Newick formatted file with any extension.
MATLAB opens a second Phylogenetic Tree Tool window with tree data from the selected file.
Use the Open command to read tree data from a Newick formatted file and display that data in a Phylogenetic Tree Tool.
From the File menu, click Open.
The Select Phylogenetic Tree File dialog box opens.
Select a directory, select a Newick formatted file, and then click Open. The Bioinformatics Toolbox uses the file extension .tree for Newick formatted files, but you can use any Newick formatted file with any extension.
MATLAB replaces the current tree data with data from the selected file.
Use the Import from Workspace command to read tree data from a phytree object in the MATLAB workspace and display that data in a Phylogenetic Tree Tool.
From the File menu, click Import from Workspace.
The Get Phytree Object dialog box opens.
From the list, select a phytree object in the MATLAB workspace.
Click the Import button.
MATLAB replaces the current tree data in the Phylogenetic Tree Tool with data from the selected object.
There may be sometimes when you make changes that you would like to undo. Phytreetool does not have an undo command, but you can get back to the original tree you started viewing with the Restore Original Tree command.
From the File menu, click Restore Original Tree.
A new phytree tool window opens with the original tree.
After you create a phytree object or prune a tree from existing data, you can save the resulting tree in a Newick formatted file. The sequence data used to create the phytree object is not saved with the tree.
From the File menu, click Save As.
The Save Phylogenetic tree as dialog box opens.
In the Filename box, enter the name of a file. The Bioinformatics Toolbox uses the file extension .tree for Newick formatted files, but you can use file extension.
Click Save.
phytreetool saves tree data without the deleted branches, and it saves changes to branch and leaf names. Formatting changes such as branch rotations, collapsed branches, and zoom settings are not saved in the file.
After you have explored the relationships between branches and leaves in your tree, you can copy the tree to a MATLAB figure window. Using a figure window allows you to use all the MATLAB features for annotating, changing font characteristics, and getting your figure ready for publication. Also, from the figure window, you can save an image of the tree as it was displayed in the Phylogenetic Tree Tool window.
From the File menu, point to Print to Figure, and then click either With Hidden Nodes or Only Displayed.
The Publish Phylogenetic Tree to Figure dialog box opens.
Select one of the Rendering Types, and then select the Display Labels you want on your figure.
Square (square branches)
Angular (angular branches)
Radial
Select the Display Labels you want on your figure. You can select from all to none of the options.
Branch Nodes — Display branch node names on the figure.
Leaf Nodes — Display leaf node names on the figure.
Terminal Nodes — Display terminal node names on the right border.
Click the Print button.
A new figure window opens with the characteristics you selected.
Because some of the Phylogenetic Tree Tool commands cannot be undone (for example, the Prune command), you might want to make a copy of your tree before trying a command. At other times, you might want to compare two views of the same tree, and copying a tree to a new tool window allows you to make changes to both tree views independently .
From the File menu, point to the Export to New Tool submenu, and then click either With Hidden Nodes or Only Displayed.
A new Phylogenetic Tree Tool window opens with a copy of the tree.
Use the new figure to continue your analysis.
The Phylogenetic Tree Tool can open Newick formatted files with tree data. However, it does not create a phytree object in the MATLAB workspace. If you want to programmatically explore phylogenetic trees, you need to use the Export to Workspace command.
From the File menu, point to Export to Workspace, and then click either With Hidden Nodes or Only Displayed.
The Export to Workspace dialog box opens.
In the MATLAB variable name box, enter the name for your phylogenetic tree data.
Click OK.
MATLAB creates an object in the MATLAB workspace with type phytree.
When you print from the Phylogenetic Tree Tool or a MATLAB figure window (with a tree published from the tool), you can specify setup options for printing a tree.
From the File menu, click Page Setup.
The Page Setup - Phylogenetic Tree Tool dialog box opens. This is the same dialog box MATLAB uses to select page formatting options.
Select the page formatting options and values you want, and then click OK.
Use the Print Setup command with the Page Setup command to print a MATLAB figure window.
From the File menu, click Print Setup.
The Print Setup dialog box opens.
Select the printer and options you want, and then click OK.
Use the Print Preview command to check the formatting options you selected with the Page Setup commend.
From the File menu, click Print Preview.
A window opens with a picture of your figure with the selected formatting options.
Click Print or Close.
Use the Print command to make a copy of your phylogenetic tree after you use the Page Setup command to select formatting options.
From the File menu, click Print.
The Print dialog box opens.
From the Name list, select a printer, and then click OK.
| | Opening the Phytreetool GUI | Tools Menu | |
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