The Tree Viewing Window

The tree viewing window is opened when a tree has been calculated from an alignment, or imported via a file or web service. It includes menus for controlling layout and file and figure creation, and enables various selection and colouring operations on the associated sequences in the alignment.

Selecting Sequence Leaf Nodes
Selecting sequence ids at the leaves of the tree selects the corresponding sequences in the original alignment. These selections are also reflected in any other analysis windows associated with the alignment, such as another tree viewer.

Grouping sequences by partitioning the tree at a particular distanec
Clicking anywhere along the extent of the tree (but not on a leaf or internal node) defines a tree 'partition', by cutting every branch of the tree spanning the depth where the mouse-click occurred. Groups are created containing sequences at the leaves of each connected sub tree. These groups are each given a different colour, which are reflected in other windows in the same way as if the sequence ids were selected, and can be edited in the same way as user defined sequence groups.

Tree partitions are useful for comparing clusters produced by different methods and measures. They are also an effective way of identifying specific patterns of conservation and mutation corresponding to the overall phylogenetic structure, when combined with the conservation based colour scheme.

Selecting Subtrees and changing the branch order and subtree group colour
Moving the mouse over an internal node of the tree will highlight it. You can then :

• Click the highlighted node to select all the sequences in that branch.
• Double-click the highlighted node to rearrange the tree diagram by inverting the branch ordering at that node.
• Right-click to open the 'Select Sub-Tree Colour' dialog box, to pick a new colour for the sub-tree and associated sequences.

File Menu

This menu allows the displayed tree to be saved as a Newick tree file (Save→Newick File), printed or exported as an image (PNG) or Postscript file. Finally, data used to calculate the tree can be retrieved with the 'Input Data...' entry.

View Menu

When the tree viewer is opened, it displays all the annotation associated with a tree. Trees calculated by Jalview have branch lengths, which correspond to the distance measure used to construct the tree. Tree imported from outside may also contain bootstrap information, and additional leaves from sequences not present in the associated alignment.

The view menu mostly contains options controlling the way a tree is rendered and labeled:

• Fit to Window

  The tree layout will be scaled to fit in the display window. You may need to reduce the font size to minimise the leaf label overlap when this option is selected.

• Font Size ...n

  Brings up a dialog box to set the font size for the leaf names. n is the current font size.

• Show Distances

  Labels each branch or leaf with its associated branch length.

• Show Bootstrap values

  Labels each branch or leaf with its associated bootstrap value.

• Mark unlinked leaves

  Toggles the display of a '*' at the beginning of a leaf label to indicate that there is no sequence corresponding to that leaf in the associated alignment.

• Sort Alignment By Tree

  Sorts any associated alignment views using the current tree. (Only available in the Jalview Desktop)

• Associate Leaves with ...

  Only visible when there are multiple views of the same alignment to show and edit which alignment views are associated with the leaves of the displayed tree.