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 :
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. +
+