The MST Clusters and the visual appearance of a Minimum Spanning Tree (MST) can be modified using this window. The window contains three tabs for different groups of settings.


Cluster settings in the MST Options Window

Cluster Definition

  • Calculate Clusters: check to enable the calculation and visualization of clusters in the MST. For comparison tables that use only cgMLST distance columns, the cluster calculation is enabled by default.
  • Maximum distance in Cluster: The maximum distance two nodes can have if they are considered to be in the same cluster. For comparison tables that use only cgMLST distance columns, the CT distance is used as default for the maximum cluster distance.
  • Minimum number of Samples/Nodes: The minimum number of Samples or MST Nodes (specified below) that are required for a cluster.
  • Use for minimum: Select if minimum calculation above should use Samples or MST Nodes (=circles).
  • Order Clusters by number of Samples or MST Nodes: The cluster name consists of the defined prefix and a number. The numbering is either ordered descending by the number of Samples in a cluster or by the number of MST Nodes.
  • Highlight clusters with background color: Clusters are displayed by highlighting the nodes in a clusters. The colors of this highlights can be generated automatically or a single color can be set for all clusters (default is gray).

Cluster Labels

  • Show Cluster labels: Defined if the cluster names should be shown as labels in the MST.
  • Name prefix: The name of a cluster consists of this prefix (by default "Cluster") followed by an incrementing number.
  • Cluster label font: Choose the font and size that is used to display the label.
  • Cluster label color: Choose the color that is used to paint the cluster label.
  • Distance from label to founder: Defines how close a cluster label is located to the founding node (default: 1).
  • Draw box around label: Check to draw a box around the cluster label

Connection Lines

Optionally lines can be drawn from the cluster label to the 'founder' of the cluster. If line style is other than none, the line color and line width can be specified.


Distance number with (top) and without (bottom) white outline.

This tab allows to change how distance information is displayed.

  • Use logarithmic scale for line length > XX: If checked, a logarithmic scaling is used to determine the length of the connection lines for all lines longer than XX. Note that after changing this options the MST will be re-layouted.
  • Show distance numbers: Check to show distance numbers next to the connection lines.
  • Font/Color: Change font, size and color of the distance numbers.
  • Draw white outline: Should a small white outline be drawn around the distance number?
  • Line style: This allow to specify which line style can be used for which distances.


Separator lines example.
Frequency displayed using colors (left) and node size (right).

This tab allows to change how the tree nodes are displayed.

  • Fill node colored by group: Check to color nodes according to the groups. If a node contains multiple Samples in a different group, the color information is presented as pie-chart.
  • Draw node border colored by group Use a slightly darker variant of the color group for painting the node border.
  • Draw separator lines: Only available if frequency is not displayed using colors. Adds small separator lines into the Circles to display the Sample count.
  • The number of Samples in a node/genotype can be displayed using colors or by changing the size of the nodes. Six different colors can be used to display the number of Samples using color. If the number of Samples is displayed using the size of a node, the minimal size, the maximum size of the node and how much the size is increased for each Sample in a node can be specified.
  • Node label This allow to change font, size and color of the node label. If the node label is longer than a given number of characters, it is abbreviated. The thin white outline that is painted around the label text can be switched off.