Sequence Dendrogram Panel Features

• Settings button
  • Tree layout option menu
  • Computation settings section
    • Relationship metric option menu
    • Similarity matrix option menu
    • Tree type options
    • Reset button
    • Recalculate Tree button
• Reload link
• Dendrogram display area
• Save Image button

Settings button

Click this button to make settings for the calculation and appearance of the dendrogram. Opens the settings pane, which has the following features:

Tree layout option menu

Choose the layout for the tree, from Rectangular or Radial.

Computation settings section

Make settings for the computation of the dendrogram.

Relationship metric option menu

Calculate the relationships between the sequences that are used to construct the dendrogram using one of the following metrics. The choice is displayed to the left of the settings button when the tree is recalculated.

• Identity %—use sequence identity
• Similarity %—use sequence similarity based on a chosen similarity matrix type

Similarity matrix option menu

Choose the similarity matrix family to use for calculating the similarity of the sequences. The matrix actually used depends on the sequence similarity. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848038/ for information on how to choose a matrix family. The choices are:

• BLOSUM
• PAM
• GONNET

Only available when Similarity is chosen from the Relationship matrix option menu.

Tree type options

Choose the method for tree construction. Both available methods are iterative clustering methods, where (in this case) branches are merged (clustered) on the basis of similarity.

• Neighbor-joining—join branches in the tree that have the largest similarity. This method considers not the only distance between pairs of branches to be merged but also how far the branches are from all others. Pairs that are close to each other but far away from others are merged first.
• UPGMA (average distance)—join branches in the tree that have the smallest average distance. If two pairs of branches have the same (or very similar) distances, the choice of which to merge first is made arbitrarily.

Reset button

Reset the computation settings to their default values.

Recalculate Tree button

Click this button after changing the settings to recalculate the tree.

Reload link

Reload the dendrogram for the current view. This link is active when changes have been made in the view, such as adding sequences, that make the dendrogram out of date.

Dendrogram display area

Displays the dendrogram. Each sequence is labeled with the PDB ID and chain. You can click a sequence or its label using the left mouse button to select it in the Multiple Sequence Viewer/Editor; the sequence label is outlined to indicate selection, and the number of selected sequences is displayed at the lower right.

Selecting sequences in the Multiple Sequence Viewer/Editor also selects them in the dendrogram. The label is also displayed as a tooltip on the termini of the dendrogram. To zoom in to one or more branches in the dendrogram, click on the branch labels to select them, then right click and select Zoom to Selected. To zoom out, right click again and select Reset View.

Hovering over a branch of the dendrogram shows a tooltip listing all of the sequences in the branch and the distance with 4 decimal places of precision. If there are more than 15 sequences in a branch, the remaining “N” number of sequences are denoted with "(and N more)” in the tooltip.

You can click and drag the right mouse button to translate the dendrogram. On a standard 3-button mouse, you can use the mouse wheel to zoom in and out of the display. On a touchpad, you can drag with two fingers to zoom in and out of the display.

Save Image button

Save an image of the dendrogram in PNG or PDF format, at a chosen resolution. Opens a file selector in which you can navigate to a location and name the file.