Export a tree to a tree viewer

As described in Export data to a file, Phylogenetic trees can be exported in Newick (.newick) or Nexus (.nex, .nxs) formats using File > Export Data > Tree. The saved files can be opened by many free and commercial evolutionary biology software programs.

The following procedure goes a step further. It lets you automatically launch a third-party tree viewer and view the tree within that application.

To export and open the phylogenetic tree in a third-party tree viewer:

1. Outside MegAlign Pro, download the desired tree viewer and install it on your computer. Compatible viewers include Archaeopteryx (Win only) and FigTree.

*Note: When installing FigTree on a Macintosh computer, you may receive a message that the application is damaged. You may need to change your Security & Privacy settings to allow applications downloaded from “Anywhere” prior to installation.

2. In MegAlign Pro, set the default application for opening saved trees using the File > Send Tree To menu command.

3. Perform an alignment.

4. Export the tree using File > Send Tree to (Tree Viewer). If you have chosen a compatible tree viewer, this command launches the viewer with the active MegAlign Pro project tree open. If a tree viewer has not yet been specified, you will receive the following message:

Click OK to launch the application preferences dialog, where you can indicate the viewer location.

*Note: If you export a tree containing duplicate sequence names, you may receive a warning when you try to open it in a third-party application. To fix this issue, return to MegAlign Pro, rename one of the sequences, and then re-export the tree.