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 distance
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. A red line will be shown where the partition was made, and 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.To distinguish parts of the alignment assigned to different groups, you may also enable the Sequence ID colour scheme via the Alignment window's Colours menu (Since 2.11).

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 :

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: