Both phylogenetic trees and MSA guide trees can be saved as pictures, or printed.
If a phylogenetic tree has been generated, it will be saved when you save its associated MSA file, so that when you reload the MSA file and select the phylogenetic tree button, the Tree Viewer will open and display the tree. Any rooting, rotating, deleting and reformatting you have done is retained when you save the MSA file.
In addition, it is often useful to save an image of the tree as it appears in the Tree Viewer window. When the Tree Viewer window is active, you can use Edit | Copy to copy the tree to the clipboard. You can then paste it into another application as a PDF. A good tip is to open Preview and go to File - New From Clipboard
An important function of the Tree Viewer is to provide publication-quality printed output. To keep the interface simple to use, the phylogenetic tree display is always scaled to fit the width of the selected paper size. You can set the page size with File | Page Setup, and view the page boundaries in the Tree Viewer window, using the page mode button in the bottom left corner.
1. With the Tree Viewer window active, choose File | Print.
A printing dialog box is displayed.
2. Set the printer controls, and select Print to print the tree.