The Tree Viewing Window

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftreeviewer.html;h=638ed3c3a5d96d614f92fad055d5d66d01b821a6;hb=c9bcd60e5ed0681116e9bedbd371f7a8b8290126;hp=f05572c9564775069a5eb8d3f1431f3be5edbdbb;hpb=85fb1c79fd82d7eada801624f745635632be8362;p=jalview.git diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index f05572c..638ed3c 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -1,32 +1,39 @@ + The Tree Viewing Window

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.

- -

Moving the mouse over an internal node of the tree will highlight - it. You can then :

Click the highlighted node to select all the sequences in that branch. -
Double-click the highlighted node to rearrange the tree - diagram by inverting the branch ordering at that - node. -
Right-click to open the 'Select Sub-Tree Colour' dialog box, to - pick a new colour for the sub-tree and associated sequences. -

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 @@ -42,7 +49,20 @@ 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 :

Click the highlighted node to select all the sequences in that branch. +
Double-click the highlighted node to rearrange the tree + diagram by inverting the branch ordering at that + node. +
Right-click to open the 'Select Sub-Tree Colour' dialog box, to + pick a new colour for the sub-tree and associated sequences. +

+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 @@ -56,21 +76,21 @@ 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 view menu mostly contains options controlling the way a tree is +rendered and labeled:

Fit to Window
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.
Font Size -n
+
Font Size ...n
Brings up a dialog box to set the font size for the leaf names. n is the current font size.
Show Distances
-Labels each branch or leaf with its associated branch length. -

Show Bootstrap values
Labels each branch or leaf with its associated bootstrap value.

Leaf Association
-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. -
-

Sort Alignment By Tree +

+ Sorts any associated alignment views using the current tree. (Only + available in the Jalview Desktop) +

Associate Leaves with ... +

+ 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. +