X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftreeviewer.html;h=8cb2b59e23be8ea21c2b2a515c9b20f298a5f54a;hb=383fd91269f510b189450fbe174e9c051103c7eb;hp=b45f8fed99c72733f6a9da03fd3037c7a19a4022;hpb=c17661b22323a66090ea91e04751aa17461b17c5;p=jalview.git diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index b45f8fe..8cb2b59 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -28,29 +28,28 @@
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. + href="tree.html">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
+ 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
+ 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
+ in the same way as if the sequence IDs were selected, and can be
edited in the same way as user defined sequence groups.
@@ -59,7 +58,10 @@ identifying specific patterns of conservation and mutation corresponding to the overall phylogenetic structure, when combined with the conservation - based colour scheme. + 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
@@ -95,23 +97,24 @@
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. 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 branch
+ length. Labels each branch or leaf with its associated bootstrap
+ 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. 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
@@ -120,10 +123,9 @@
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.
+ href="../features/multipleViews.html">multiple
+ views of the same alignment to show and edit which alignment
+ views are associated with the leaves of the displayed tree.