Screenshot of the Phylogenetic Tree Window. Selected Samples are highlighted by a red dotted outline. Table data is included in the tree image.
Dendrogram (left), circular tree (middle) and radial tree (right).

This window contains a phylogenetic tree for the Samples currently displayed in the Comparison Table. The tree is linked with the table. Any changes and selections in the table will update the tree.
Only one linked phylogenetic tree window can be opened for each comparison table. However, to make comparison of different trees or different settings possible, the window can be disconnected from the table, which allows to open another phylogenetic tree window.

Trees can be displayed as three different types of graphs:

  • a dendrogram or
  • a circular tree or
  • a radial tree

Two tree types are supported:

  • Neighbor-Joining Tree (Saitou, Nei 1987)
  • UPGMA Tree (Sokal, Michener 1958)

The Zoom Controls can be used to zoom the graphs or to increase the length of the lines. The trees can be exported in various formats.

To select Samples in the tree, either click each leaf or click an inner node to select all Samples in the subtree below the node. Hold the CTRL-key to select multiple Samples. Click on a Sample using the right mouse button to open a context menu.

Distance calculation

The tree is built using the values from the columns that are selected for distance calculation. If the columns used for distance calculation change, the tree is rebuilt (if the window is not disconnected from table).

Empty values or values that start with a ? are treated as missing values. Depending on the Distance Calculation Settings these missing values are either treated as an own category or ignored during pairwise comparison. The Distance Calculation Settings command can be used to change the settings.

For a lower number of columns for distance calculation, (e.g. for MLVA data or MLST data), the missing values are an own category option is recommended. For a larger number of columns (e.g. cgMLST with thousands of targets) the pairwise ignore missing values option is recommended.

Note that the option pairwise ignore missing values may result in problems in the tree when a Sample contains many missing values. It is recommended to remove Samples that have missing values in more than 10% of the columns for distance calculation before calculating a tree.



  • ExportTree.gif Export Tree: Allows to export the tree and the graph in various formats:
    • PNG: Exports a raster-image in the currently displayed resolution.
    • SVG: Exports a vector graphic image that can be resized without loss of quality. The SVG-format is well suited for creating high-resolution graphics. See Image File Formats for more information.
    • NWK: Newick Tree Format. Contains a textual representation of the tree that can be viewed by other programs, e.g. MEGA.
  • UpgmaTree.png UPGMA-Tree: Display an UPGMA-tree.
  • NjTree.png NJ-Tree: Display a NJ-tree.
  • Button16-Chain.gif Disconnect Tree from Table: Changes in the table will not update the tree any more. Opening a new tree window is possible after disconnecting. This option can be used to compare trees for different data or settings. Note that the label text cannot be changed after the tree is disconnected and that additional data is removed from the tree.


  • Dendrogram.png Dendrogram View: Displays the tree as a dendrogram.
  • Circular.png Circular View: Displays the tree as circular graph.
  • Radial.png Radial View: Displays the tree as radial graph.
  • ZoomControls.gif Show Zoom Controls: Toggles the visibility of the zoom controls for zoom and line length.
  • Options.png View Options: Opens a dialog window that allows to customize how the tree is displayed. The font and color of the labels can be selected and it is possible to specify if boxes should be drawn around labels.
  • Show distance matrix: Opens a window with the distance matrix that was used for building the tree and allows to export this distance matrix in MEGA or NEXUS format (e.g. for use with the SplitsTree software).
  • LabelColumns.png Choose Columns for Label: Select the columns that are used for the tree labels. More than one column can be selected, the values are then separated by ','
  • AddDataToTree16.png Add Data to Tree: Choose columns that are included as additional data into the tree image. See Add Data to Tree.
  • Sort by Selected Nodes: If checked, the nodes that are selected in the tree window are sorted to the top of the Comparison Table.

Context menu

The context menu can be opened by right-clicking a tree node. It contains the following commands:

  • Reroot.png Reroot Tree: Sets the new root of the tree above the selected tree node.
  • Rotate.png Rotate Subtree: Only available when an inner node was clicked. Rotates the subtree below the node.
  • AddToExclude.png Add to Exclude List: Add the selected Samples to the exclude list.
  • Set Group: Allows the set the group for the selected Samples.


  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406
  • Sokal R, Michener C. A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 1958, 38:1409–1438.