The Tree Viewing Window
-- When a tree has been calculated from an alignment, or imported via a - file or web service it is displayed by Jalview's tree viewing - window. Trees can be rearranged, used to select sequences and groups - in the associated alignment, saved in Newick format or exported as an - image or postscript file.
-- 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.
- -Moving the mouse over an internal node of the tree will highlight - it. You can then :
+ 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 :
+
- 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.
-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 contains options controlling the way a tree is -rendered and labelled: -
-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. -
-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. -
-+ 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. +
+