- 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. 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: -
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.
- Brings up a dialog box to set the font size for the leaf names. - n is the current font size. -
Labels each branch or leaf with its associated branch - length.
Labels each branch or leaf with its associated bootstrap - value.
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.
- Sorts any associated alignment views using the current tree. (Only - available in the Jalview Desktop) -
- 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. -
-