SIMMAP | modifying trees

Tree Modifications (Manipulations)

SIMMAP offers a number of options for modifying how trees are displayed in the Tree View window and for constraining a character history analysis. To activate Tree Modifications you can use the keyboard shortcut [

L], or select Turn On Tree Modifications in the Trees main menu item. Once selected the text in the top right of the Tree View window (shown below) becomes red and reads Modifications:ON.

The following options are available (from top to the bottom of the window shown above):

The first item listed in window shown after activating tree modifications is the node being selected. This is reported as the node number an arbitrary numbering of the nodes in the displayed tree. To verify that you have selected the correct node you can display the node numbers by selecting Display Tree Node Indices [N] in the Trees item in the main menu.
Fix Ancestral States - This option will select the node to be fixed for a particular or subset of possible states. The following window will be displayed at the top of the Tree View window (shown directly below).

Using this window the user can Select a Site (character) to fix states for the selected node. The options will be dependent on the datatype (molecular or morphological) and the number of possible character states (4 for molecular data and from 2 to up to 7 for morphological data). The user can select one or mutliple states to fix or constrain the possibilities for the node. If one option is selected then the node will be constrained to have a prior probability of 1 for that state. If the user selects more than one state but less than the total number of possible states the prior probability will be divided equally among the chosen states and zero for unchosen states. If all states are chosen then all states are considered possible. This, of course, is the default in SIMMAP in which all states are possible.

To fix a state simply select the Fix button. Otherwise, select the Cancel button to disregard the selected options.
Unfix Ancestral States - This option negates any previous fixing of ancestral states at the selected node. This option is only available if the states at the node have been previously fixed.

From the window the user can select to remove the ancestral constraints at a particular site (character). To select a site or character to remove the ancestral constraint from select the site number from button to the right of Select a Site to Unfix text in the window.

To remove, or unfix, a particular character select Unfix button. Otherwise, select the Cancel button to disregard this action.
Create Constraint - This option allows the user to create a node constraint that allows the ancestral states for this node to be calculated. This feature is dealt with in the help documents on calculating ancestral states.
Rotate Node - The user can select to rotate a node and its descendant taxa. An example of rotating a node is shown below (the rotated node is highlighted by a red dot). The right half of the image is the tree prior to rotation while the left side of the image is the tree after rotation. This option is an absolutely asthetic option and does not affect any analyses. This option is useful if you wish to save the tree to a file for publication or to print the tree.
Mark Node - As with the previous option, this option is aesthetic. The user can opt to mark a node and select that the node is displayed with a dot (using whatever color is chosen, see the help documents for setting SIMMAP preferences on how to change this. The node mark is shown below in the default red).


	Help Documentation Current document


	Tree Modifications (Manipulations) SIMMAP offers a number of options for modifying how trees are displayed in the `Tree View` window and for constraining a character history analysis. To activate Tree Modifications you can use the keyboard shortcut [L], or select `Turn On Tree Modifications` in the `Trees` main menu item. Once selected the text in the top right of the `Tree View` window (shown below) becomes red and reads `Modifications:ON`. The following options are available (from top to the bottom of the window shown above): The first item listed in window shown after activating tree modifications is the node being selected. This is reported as the node number an arbitrary numbering of the nodes in the displayed tree. To verify that you have selected the correct node you can display the node numbers by selecting `Display Tree Node Indices` [N] in the `Trees` item in the main menu. `Fix Ancestral States` - This option will select the node to be fixed for a particular or subset of possible states. The following window will be displayed at the top of the `Tree View` window (shown directly below). Using this window the user can `Select a Site` (character) to fix states for the selected node. The options will be dependent on the datatype (molecular or morphological) and the number of possible character states (4 for molecular data and from 2 to up to 7 for morphological data). The user can select one or mutliple states to fix or constrain the possibilities for the node. If one option is selected then the node will be constrained to have a prior probability of 1 for that state. If the user selects more than one state but less than the total number of possible states the prior probability will be divided equally among the chosen states and zero for unchosen states. If all states are chosen then all states are considered possible. This, of course, is the default in SIMMAP in which all states are possible. To fix a state simply select the `Fix` button. Otherwise, select the `Cancel` button to disregard the selected options. `Unfix Ancestral States` - This option negates any previous fixing of ancestral states at the selected node. This option is only available if the states at the node have been previously fixed. From the window the user can select to remove the ancestral constraints at a particular site (character). To select a site or character to remove the ancestral constraint from select the site number from button to the right of `Select a Site to Unfix` text in the window. To remove, or unfix, a particular character select `Unfix` button. Otherwise, select the `Cancel` button to disregard this action. `Create Constraint` - This option allows the user to create a node constraint that allows the ancestral states for this node to be calculated. This feature is dealt with in the help documents on calculating ancestral states. `Rotate Node` - The user can select to rotate a node and its descendant taxa. An example of rotating a node is shown below (the rotated node is highlighted by a red dot). The right half of the image is the tree prior to rotation while the left side of the image is the tree after rotation. This option is an absolutely asthetic option and does not affect any analyses. This option is useful if you wish to save the tree to a file for publication or to print the tree. `Mark Node` - As with the previous option, this option is aesthetic. The user can opt to mark a node and select that the node is displayed with a dot (using whatever color is chosen, see the help documents for setting SIMMAP preferences on how to change this. The node mark is shown below in the default red).


	Page Last Updated: 6 August 2008