MacVector's Tree Viewer window lets you display and edit phylogenetic trees and ClustalW guide trees.
You can choose between alternative display styles, and adjust the formatting for printed output. When you have edited a tree, you can re-order the MSA sequence to match the tree.
You can edit a phylogenetic tree in a Tree Viewer window by rooting, rotating and deleting, using the toolbar buttons. You can also format the fonts and lines used in the display, and control the display of branch and node labels. When a tree is saved along with its MSA file, any editing you have applied to it is retained.
NOTE: If you have deleted part of a tree, the phylogeny will have been recalculated, so it no longer represents the full MSA file.
Although both CLUSTALW guide trees and Phylogenetic trees can be displayed in Tree Viewer windows, there are important differences in the way MacVector treats ClustalW guide trees and phylogenetic trees. Both can be edited by rooting and rotating, but ClustalW trees cannot be changed by deleting, because they cannot be recalculated. Phylogenetic trees retain all editing and formatting changes, when their associated MSA files are saved: ClustalW guide trees, on the other hand, lose all editing changes when their MSA files are saved.
The same phylogenetic data can be displayed in any of three styles:
- Slanted cladogram
- Rectangular cladogram
- Phylogram
Only the phylogram display mode draws branch lengths to scale, indicating evolutionary distance. This mode is not available for bootstrap consensus trees.
An important property of a tree is its polarity. The neighbor joining method of generating trees makes no assumption about which sequence is closest to the ancestral sequence, and in which direction evolution has preceeded. This can often be clarified by rooting the tree. Rooting affects only the appearance of the tree, not the underlying phylogenetic analysis.
You can recognize an unrooted tree by its first (leftmost) junction, which is always trifurcated. In a rooted tree, the first junction is always bifurcated - it separates either the outgroup from the rest (outgroup rooting) or two aggregates from each other (midpoint rooting).
Rooting on an outgroup can often help to emphasize groupings. Where there is no obvious outgroup, midpoint rooting may be useful. This method works by sampling each internal node, calculating the sum of all branch lengths under the nodes to the left and right of it. Where these two sums are most nearly equal, the midpoint is identified, at the "center of gravity".
You can root a tree from a selected outgroup by using the rooting button. Alternatively you can specify outgroup rooting in the Tree Viewer Options dialog box, in which case MacVector will root the tree on its longest terminal node. To specify midpoint rooting, use the Tree Viewer Options dialog box.
The rooting of trees generated using UPGMA cannot be changed. ClustalW guide trees can be rooted.
1. In the Tree Viewer window, select the required outgroup by clicking on its branch (click on the line, not the label).
The branch becomes highlighted, and the rooting button becomes active.
TIP: Ensure that only one sequence is highlighted. You can only root the tree on a single sequence.
2. Select the rooting button.
Alternatively, choose Analyze | Phylogenetic Analyses | Root Tree on Node.
The tree is shown rooted on the selected outgroup.
You can also specify outgroup rooting by using the Tree Viewer Options dialog box.
You can delete a node from a phylogenetic tree. The tree is recalculated automatically, excluding all sequences contained in the node.
1. In the Tree Viewer window, select a node to delete by clicking on it.
The node, together with its sub-nodes, becomes highlighted. The delete node button becomes active.
2. Select the delete node button.
Alternatively, choose Analyze | Phylogenetic Analyses | Delete Node.
The tree is recalculated, with the node deleted.
NOTE: To undo a deletion, choose Edit | Undo Delete.
You can re-order the sequences in any tree diagram by rotating selected nodes through 180 degrees . Rotation flips the order of all sequences contained in the selected node. Rotating affects only the appearance of the tree, not the underlying phylogenetic analysis.
1. In the Tree Viewer window, select a node to rotate by clicking on the branch above it.
The node, together with its sub-nodes, becomes highlighted. The rotate button becomes active.
NOTE: The rotate button only becomes active when more than one sequence has been selected.
2. Select the rotate button.
Alternatively, choose Analyze | Phylogenetic Analyses | Rotate Node.
The node is rotated, flipping the order of its sequences.
3. Repeat steps 1 and 2 as required to sort the tree.