Tree Display Help

Click "Distances" to toggle whether the Tree shows numerical branch lengths, which correspond to inferred evolutionary distances. The lengths of the branches are always displayed in accord with this distance.

Click "Rotators" to show targets for rotating branch points in the Tree. When shown and clicked, these cause the branch point to be rotated. A judicious choice of rotations can often make the Tree more interpretable by the reader. These changes do NOT alter the structure of the Tree.

Click "Rerooters" to show targets for rerooting the Tree. When shown and clicked, these cause the Tree to be recalculated with a new root at the position of the rerooter clicked. Warning: this method should be used with caution as it alters the underlying tree.

Click "Names" to hide or show the sequence names on the Tree.

Click the "-" and "+" buttons to zoom out or zoom in on the tree image, respectively.

To view the distance between any pair of sequences, click one (it turns red), then shift-click the other (it turns red too). Their distance is shown in the center of the information bar at the bottom.


File Menu:

Load Tree: Load a Bonsai format tree.

Save Tree: Save a Bonsai format tree.

Import PHYLIP Tree: Read a PHYLIP format tree from a file and display in window.

Export Tree as PHYLIP: Code the current tree in PHYLIP save format and save to file.

Save as GIF: Save the tree graphic as a GIF format file. All of the currently displayed tree adornments such as distances and rotators will be included.

Save Sequences: Save the sequences that back this tree to a file in ".bnss" format. The tree must be sequence backed.

Print Tree: To print out the current tree. Any optional labels that are showing will be printed as well.


Edit Menu:

Tree Font Size: sets the font sizes on the tree. Fonts for all displays change coordinately.

Remove Selected Leaves: Select leaves by Cntrl-clicking the sequence names. The name will change to bold blue font. This menu command deletes all the selected leaves and recalculates a new tree from the remaining sequences.

Clear Selections: Clear all tree selections. Selection methods are not carefully implemented yet and you may use this to clear confused selection states as well.

Clear Bootstrap Values: Use this if you have computed the bootstrap but no longer want to display the values on the tree.

Duplicate this Frame: Duplicates the frame AND the entire underlying tree data set.


Show Menu:

Tree Properties: show a panel with properties of the current tree.

Sequence List Properties: show a panel with basic information about all the sequence leaves.

Distance Corrector: Show a frame that displays (and permits changes in) the values used to correct raw distance values to compute the phylogenetic tree.

Distance Table: show a table of the pairwise sequence distances that underlie this tree. The table will show the distance type that you select in the submenu.

Score Table: show a table of all pairwise raw alignment scores. For this and other tables here there is a display issue that is problematic if you are have a lot of columns. I will resolve this soon but for now, try making the table as big as possible and moving column header borders around with the mouse.

Percent ID Table: show a table of all the pairwise percent residue identity values.

Matrix Table: show a table of the score matrices used for each pairwise alignment that underlies the distances for this tree. These will usually have been selected dynamically by Bonsai to match the comparison.

Turbo Words Score Table: show a table of all the pairwise Turbo Words scores that were used to select score matrices for the pairwise alignments.


Tree Menu:

Recompute: Recomputes the underlying tree and it's display according the currently selected tree parameters.

Recompute From: Recomputes the underlying tree and it's display according the tree parameter selected from the submenu.

Compute Bootstrap: To compute bootstrap statistics for the current tree. A dialog will appear that lets you choose the number of bootstrap repeats. At least 1,000 is recommended to get reasonably accurate statistics. The bootstrap is a method for assessing the statistical robustness of the positions of branches in a tree. In essence, for a single bootstrap, the pairwise sequence alignment scores are allowed to vary stochastically and a new tree is built from those scores. This is repeated a large number of times and the frequency at which various tree topological features appear is counted. This value will appear on each branch of the tree display as a percentage. 100% means a perfectly robust branch (one that appears on every bootstrap tree), and a low percent means the opposite.

Find 'Best' Root: [NOTE - this is not an objectively "correct" root.] The Neighbor-Joining method roots trees arbitrarily, producing a fundamentally unrooted tree with a "pseudoroot". The Best Root method takes an existing tree and finds the root position that produces the most uniform distance to all the leaves. This isn't guaranteed to be the correct phylogenetic root unless the molecular clock is constant, but it generally does fairly well even if the clock is somewhat inconstant. [ add notes on what it does ]

Compute Distance/Tree Fit: Calculate how exactly this tree represents the underlying pairwise distance data. If the match is perfect, this value will be 0. Most pairwise distance data cannot be represented perfectly by a single tree, but usually it will be a close fit.

Compute Leaf Dispersion: Calculate the extent to which the tree leaves deviate from perfectly aligned (in the same vertical position on the display). If the molecular clock is constant, selection has not played a differential role in various lineages, and the sequences are long enough to minimize stochastic deviations, this number will be close to 0.


Align Menu:

Align All Sequences: If the tree is backed by pairwise alignments, you can use the displayed tree as the guide tree for a progressive multiple sequence alignment.

Align Selected Sequences: Similar to Align All, but aligns only the subset of sequences that are currently selected.


Settings Menu:

Tree Settings: Show the current settings used to construct this tree.

Multiple Alignment Settings: Show the current settings for a multiple aligment. These will initially reflect the settings used during the alignment that created this tree, and they can be edited for used in future multiple alignments.


Help Menu:

Tree Display Help: This help.

Understanding Trees: A guide to understanding how trees are computed and displayed in Bonsai and what they mean. Link.


James H. Thomas, Department of Genome Sciences, University of Washington
7/31/2002