A Tree Set is a collection of phylogenetic trees that are to be processed together by MorphoJ to assess the consequences of phylogenetic uncertainty on comparative analyses of shape. Tree Sets are only used by the method for Collect Statistics on Tree Set.
Each Tree Set is imported into MorphoJ from a single NEXUS file containing a single TREES block with multiple TREE commands. The file is read in the same way as individual trees are read with Import Phylogeny, except that the trees from all TREE commands are kept together as a Tree Set. All trees in the TREES block must contain the same set of taxa.
Choosing the menu item Import Phylogeny Tree Set in the File menu will invoke the following dialog box:
The dialog box presents a text box for entering a name for the Tree Set and an interface for choosing a NEXUS file containing the Tree Set from the computer. Clicking the Open button will select the file an import it into MorphoJ.
As a result, the Tree Set will appear in the Project Tree, named according input provided in the text field.
To examine the trees, you can invoke the popup menu for the Tree Set and select 'Display Graphs'. The first tree in the Tree set will appear in the Graphics window. To select another tree, invoke the pop-up menu of the graph and use the first entry, Select the Tree to Display. This will bring up a dialog box like the following, where you can select any tree from the Tree Set:
MorphoJ checks whether all the trees in the NEXUS file are associated with the same set of taxa. If not, an error message is displayed in the Reports window and the import process is aborted. In this case, the Tree Set will not appear in the Project Tree.
MorphoJ only reads the relevant part of the information in a NEXUS file and ignores the rest (see Import Phylogeny File for more details). For reading Tree Sets, trees are read from a single TREES block (the first to appear in the NEXUS file; any other TREES blocks are ignored). Taxon names are obtained in the same way as for importing single phylogenies (see Import Phylogeny File for more details).
Maddison, D. R., D. L. Swofford, and W. P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46:590–621.