+ 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: +
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. +
+