X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Ftreeviewer.html;h=f98ea5d1c5b963bc7b8425fe4467a5e573cda71f;hb=eea2b610bea04896964d403093df1141a16efd5f;hp=3f855ac99fa98ffd2fce4c5636a4d6de6d1781d0;hpb=8ee7a0f79f6da26d5011c60a80226d6994733cab;p=jalview.git diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index 3f855ac..f98ea5d 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -5,72 +5,88 @@
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.
+ 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.
- Clicking on an internal node of the tree will rearrange the tree - diagram, inverting the ordering of the branches at that node. -
-+
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 occured. Groups
+ of the tree spanning the depth where the mouse-click occurred. Groups
are created containing sequences at the leaves of each connected
- subtree. These groups are each given a different colour, which are
+ 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 clusterings produced by +
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
+
+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. +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, -or additional leaves from sequences not present in the associated -alignment. +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. +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. +