Color tips in the tree that are unique to certain groups of samples. Internal nodes where all descendants are unique to a group are themselves considered unique to that group.
If checked, collapse all clades whose members share the same sample metadata value.
Color nodes in the tree based on feature metadata: for example, taxonomic annotations.
If checked, collapse all clades whose members share the same feature metadata value.
Change how the tree is drawn.
Branch lengths
Warning: the "Ignore branch lengths" and "Make ultrametric" options display modified branch lengths that can be useful for aesthetics. The resulting trees should not be interpreted with respect to their branch lengths.
The branch lengths shown correspond to the branch lengths in the original tree.
If checked, all branches are drawn with the same length. Note that the root node is never drawn with any length, regardless of if this is checked or not.
If checked, branch lengths will be adjusted so that the root-to-tip distance is the same for all tips.
Clade sorting
Annotate tips by metadata.
Barplots are only supported in the rectangular and circular layouts. Please change the layout in order to use barplots.
Color nodes in the tree that are unique to certain groups of samples (specified by the trajectory) at different timepoints throughout a gradient.
If checked, collapse all clades whose members share the same sample metadata value.
Export images of the tree and its legends. Note that PNG exports will change as the tree is zoomed and panned.
Information about the tree's topology.
| Node counts | Node lengths | |||
| Tips | Minimum | |||
| Internal nodes | Maximum | |||
| Total | Average | |||
Please note that the root node's length, even if specified, is not included in the node length statistics. Node length statistics are rounded to four decimal places.
Also note that these statistics only pertain to the tree shown here; if the tree was sheared to a table, for example, the node counts shown here will be lower than for the full tree.
Node circles
If checked, this draws circles at all nodes' positions.
Camera
Repositions the camera at the center of the tree.
If checked, the camera will automatically focus on nodes that are selected via searching by name or by clicking on an arrow in a biplot.
Clade collapsing method
The shape of the collapsed clade will show both the depth and width of the clade. This option applies to all layouts.
The shape of the collapsed clade will only show the depth of the clade but the shape will be symmetric w.r.t. to the root of the clade. This option only applies to the Rectangular and Circular layouts.
Tree coloring
If checked, tips not represented in the current sample selection are ignored when propagating the color of a clade. Applies to sample metadata coloring, animations, and sample selections in Emperor. We recommend changing this setting before starting an animation; otherwise, this setting may only be partially applied throughout the animation.