|Specify the layout of the view||Click on any of the four orientations to show the phylogenetic tree with that layout (left, up, down, right).|
|Specify the font style for selected tree leaves||Select one or more leaves, then use the Font drop-down menu to choose from available fonts. Choose More fonts to open a popup listing additional fonts. To specify the font size, type a number to the right of Font or use the corresponding up and down arrows (). Allowed values are 4 to 72. To make the font Bold and/or Italic, press the B and/or I buttons, respectively.|
|Place a colored box around selected leaves||Select one or more leaves, then check the box next to Box. Click the first square to the right of Box to specify the background color of the box. Click the second square to specify a color for the box’s border. Use the text box on the right to specify a thickness for the border.|
|Specify a color and thickness for selected branches||Select one or more branches, then click the color box to the right of Line and make a selection. Enter a number on the right to specify the thickness of the branch or use the corresponding up and down arrows (). Allowed values are 1 to 20.|
|Specify whether and how to label selected branches||Select one or more branches, then make a selection from the Branch label drop-down menu. Options include None, Distance and Name.|
|Specify the number of decimal places for the lengths of selected branches||Select one or more branches, then type a number to the right of Decimal places, or use the corresponding up and down arrows (). Allowed values are 1-7. Note that branch lengths will only change if distances were already being displayed for those branches, as described above.|
|Specify the style of selected triangles that are used to represent collapsed branches|| Collapse tree branches that are not of interest by hovering over a corresponding branch node and clicking the “minus sign” (). Uncollapse them by hovering over a triangle and pressing the “plus sign” (). Collapsed branches are represented by a triangle with text next to it showing the number of leaves in the branch.
To change the background color or outline color for a selected triangle, click the first or second box (respectively) to the right of Triangle and make selections from the color chooser. Use the text box on the right to specify the width of the outline.
To cause the triangle to be displayed at the same width as the collapsed branches had been, check the box next to Width shows maximum leaf distance. The width of the triangle before zooming is the minimum of 1) the distance from the collapsed node to the leaf farthest by distance and 2) a small constant that causes a triangle appear instead of a line. When the box is unchecked, the width of the triangle is affected only by zooming.
To make the height of the triangle proportional to the number of branches it represents, check the box next to Height varies with sequence count. When the box is unchecked, the height of the triangle is affected only by zooming.
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