Selecting branches.
To select a tree branch, the user clicks on it in a tree
panel. A selected tree branch is hatched.
To select an entire subtree, Option click on the
top branch of the subtree. To select all branches,
use 'Select All' from the 'Edit' menu (Command-A).
Holding down the Shift key while selecting branches
will add or remove them from the current selection.
All of the following examples are done on the tree from the
'Examples/SimpleAnalyses/HKY85.bf' example analysis.
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Empty Selection.
Internal labels enabled.
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Click on '6767'
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Shift-Option click on the branch
above 'Node5'
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Shift click on the branches
'719' and '136'.
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Editing Operations.
Unless otherwise noted, operations are accessed via
the 'Tree' menu or corresponding keyboard shortcuts.
Swap Subtrees
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Swap subtrees starting at selected branches
Requires two branches, which are not descendants of
one another to be selected. This operation is undoable.
If two branches being swapped are children of the
same parent, the resulting tree topology is equivalent to
the original. Otherwise, the tree topology is changed.
The operation is allowed on trees attached to
a likelihood function.
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Before Swap
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After Swap
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Collapse Branches
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Remove an internal branch and attach its children
to the parent of the branch being removed.
At least one internal branch must be selected.
For multiple branch selections, each internal
branch is collapsed.
This operation is undoable.
The tree topology is always changed by this operation.
The operation is allowed on trees attached to a likelihood function.
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Before Collapse
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After Collapse
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Delete Leaves/Subtrees
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Remove all selected leaves, and collapse all
internal branches with less than two children. Also
deletes subtrees, if a subtree is selected
Activated by pressing the Delete key, or
'Delete' from the 'Edit' menu.
This operation is undoable.
The tree topology is always changed by this operation.
The operation is allowed on trees attached to a likelihood function,
if the likelihood function is not tied to an open data panel. The
underlying datafilter will be shrunk to reflect the reduced number
of sequences.
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Before Deletion
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After Deletion
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Graft A Tip
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Add a new leaf node to each selected branch.
At least one branch must be selected.
For multiple branch selections, each internal
branch is collapsed. New leaves will receive default names,
which can later be changed. This operation is undoable.
The tree topology is always changed by this operation.
The operation is allowed on trees attached to a likelihood function,
if the likelihood function is not tied to an open data panel. Since
the tree new tree will have more leaves than the underlying data filter,
the likelihood function will be killed.
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Before Graft
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After Graft
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Reroot
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Root the tree at the selected branch.
Exactly one branch must be selected.
This operation is NOT undoable, but it always
results in the same topology in terms of ML.
The reroot can be reversed by rerooting the
tree at any of the children of the previous root.
The operation is allowed on trees attached to a likelihood function.
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Before Reroot
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After Reroot
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Unroot
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Unroot a rooted tree.
The tree must be rooted and the selection must be empty.
This operation is NOT undoable, but it always
results in the same topology in terms of ML.
The unroot can be reversed by rerooting the
tree at any of the children of the previous root.
The operation is allowed on trees attached to a likelihood function.
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Before Unroot
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After Unroot
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Balance
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Reroot an unrooted tree at a 'midpoint'.
The tree must be unrooted and the selection must be empty.
This operation is NOT undoable, but it always
results in the same topology in terms of ML.
The balance can be reversed by rerooting the
tree at any of the children of the previous root.
The operation is allowed on trees attached to a likelihood function.
Likelihood calculations are faster on balanced trees.
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Before Balance
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After Balance
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Flip tip ordering
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Swap the order of children at the selected node.
Exactly one internal branch must be selected.
This operation is undoable. It always
results in the same topology in terms of ML.
The operation is allowed on trees attached to a likelihood function.
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Before Flipping
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After Flipping
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Subtree Move
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Move the selected subtree to a different location in the tree.
A subtree (which may be a single branch) must be selected.
To move the subtree, command-click on the destination branch.
This operation is undoable.
The operation is allowed on trees attached to a likelihood function.
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Before Move
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After Move (target branch is highlighted)
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