|
|
 |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
Help Documentation
Current document |
|
|
||
|
|
Modifying The Tree Display SIMMAP offers a wide variety of options for changing how trees and character histories are displayed. This help page documents many of these features. These options are useful for visual inpsection of character histories, teaching, and producing images for presentations and publications. Modifications can be made by selecting the Tree Display Options... in the Trees main menu item, or by selecting the Display Options button at the top left of the Tree View window. A new window will be opened (if the Tree View window is open it will appear attached to the window otherwise it will appear alone). While the Tree Display Options window is open you will not be able to perform any other actions in SIMMAP.  To the right you can see the Tree Display Options window which is divided into six areas:
Labels
Show Labels At Tips Two options exist: (1) displaying the taxon labels, or (2) displaying the currently selected character states. These are displayed at the tips of the tree. Labels size Users can select the font size used in displaying labels (names or states) at the tips of the tree in the Tree View window. Press the Apply button to set the changes. Label color Users can select the font color used in displaying labels (names or states) at the tips of the tree in the Tree View window. Press the Apply button to set the changes. Show marked nodes (marked trees) Users can mark nodes that can then be displayed in the Tree View window. Marks are displayed as filled circles (see below). This options turns displaying marked nodes on and off. Further details on marking nodes see the help documents on tree manipulations (modifications).  Mark color Allows the color used in displaying marked nodes to be changed. Press the Apply button to set the changes. Codon Character Mapping Draw as amino acid translation Changes how codons are drawn when mapped in the Tree View window to amino acid coloring. This option can also be set with following keyboard shortcut [  A]. See image below for an example. Draw as codons Changes how codons are drawn when mapped in the Tree View window to codon coloring. This option can also be set with following keyboard shortcut [ S]. See image below for an example. Draw as nucleotide triplets Changes how codons are drawn when mapped in the Tree View window to triplet coloring. The topmost map represents the first codon position. This option can also be set with following keyboard shortcut [ Z]. See image below for an example. Background Color The color of the background in the Tree View window can be changed using this option. Press the Apply button to set the changes. This option does not effect saving, previewing or printing trees which uses a white background. Boundary Size Changes the boundary or buffer space placed around a tree drawn in the Tree View window. See below for an example,  Branches Default color Allows the user to change the default color used when drawing the tree when a map is not being displayed. The default color is black. Branch width Allows the user to change the width of the branches as drawn in the Tree View window. Codon States At Tips Show amino acid at branch tips When displaying the character states at the tips of the tree the amino acid residue (defined by the currently selected genetic code) is shown. A coding partition of the data must be first defined (for more information go here). Show codon at branch tips When displaying the character states at the tips of the tree the codon is shown. A coding partition of the data must be first defined (for more information go here). Optimize Multiple Sims Drawing Speed This option only has an effect when showing the character histories while simulating multiple maps. Because the drawing of the tree can often be slower than actually sampling a character history SIMMAP offers the option of optimizing the drawing speed to allow displaying of the character history to occur properly. If the trees appear improperly then selecting a slower selection will help. If you find the tree display to be fine but the analysis is proceeding to slowly then speeding up the display will reduce the computational time. A single setting will not suffice for all data sets; the more taxa will require a slower optimization setting will be needed. |
|
|
|
|
|
|
|
|
|
|
|
|
|
  Molecular Model Parameters
|
|
|
|
||
|
|
Page Last Updated: 6 August 2008 |