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Tutorial - Visualizing a Family

This page will guide you through 10 important steps for visualizing a sequence family.

  1. Select a family
  2. View the DNA/intron/protein data matrices
  3. Color by taxonomy
  4. View the tree as a cladogram
  5. Resize tree width and vertical spacing
  6. Select/exclude a subtree
  7. Highlight a subtree
  8. Reroot the tree
  9. Swap node branches
  10. View intron history
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  1. Select a family

    There are five ways to select a family for viewing:

    1. Search by family name - Search our collection of families by its formal ID or common name. (Ex: "PF00151", "Lipase")

    2. Search by sequence name - Search our collection of families by sequence taxon name. This produces a list of all families that contain this taxon. (Ex: "drosophila")

    3. Search by NCBI accession ID - Search our collection of families by the NCBI accession ID of a particular taxon. (Ex: "AAC32917.1")

    4. Upload your own family - Upload a properly formatted NEXUS file to our server. The file must contain a tree, a list of taxa, and a sequence alignment of some type.

    5. Select an uploaded family - Click on "View uploaded files" to see all uploaded data files on our server. Any family file in this list may be selected for visualization.
    		select a family

    Once you have located a family, click on the "Plot" link beside it to proceed to the plot.

  2. View the DNA/intron/protein data matrices

    NOTE: Make sure that javascript is enabled in the browser you are using. Tips for reading the plot can be found here in the docs.

    Selecting a view The default view is "Tree and Matrix," which displays the Newick tree alongside its corresponding matrix of sequence alignments. You may also choose to display only the tree or only the sequence alignment.
    Selecting a block The default alignment matrix is for the DNA sequence. To select between the different sequence alignments, click on the "Sequence" menu under "View" and select the appropriate one.
    Tree and DNA matrix After making the selections shown above, this is the resulting plot. Note that although the "Intron" data is selected, the view is "Tree only" so the intron data matrix is not shown.

  3. Color by taxonomy

    Turning on the coloring To turn on coloring, go to the the "Set Coloring" field of the menu bar and select "Taxonomy" from the drop-down menu.

    The default coloring scheme will appear. This can be changed to fit your preference. Redraw the plot to apply the coloring.

    		  Coloring on Coloring can make it easier to identify and group taxa by kingdom.

  4. View the tree as a cladogram

    Turning on cladogram To view the tree as a cladogram, check the cladogram box in the "Display Information" field of the menu bar. You can choose between normal cladogram and accelerated cladogram.

    Cladogram mode is automatically selected if no branch lengths are provided in the data file.

    Default vs. Normal vs. Accelerated cladogram

    Comparison of default mode (left), normal cladogram mode (middle), and accelerated cladogram mode (right)

  5. Resize tree width and vertical spacing

    Resized plot Tree width and vertical spacing can be set in the "Plot Formatting" field of the menu bar. Tree width scales all branch lengths relative to the length of the longest branch (in inches). Vertical spacing changes the amount of vertical whitespace between taxa.


    In this example, the tree width is changed to 3" (default: 5") and the vertical spacing is changed to 2 (default: 1). This can improve the readability of the image, especially if the tree is dense or additional text (e.g. internal node labels) is turned on.

  6. Select/exclude a subtree

    Selecting a subtree Subtree selected
    Selecting a subtree
     To select a subtree to view, click on the tree node (dots at branching points) that is the root of the subtree you want. A pop-up menu will appear, listing operations that can be performed on that particular node. Click on "Select subtree" at the top of the list.

    Excluding a subtree Subtree excluded

    Excluding a subtree
    To exclude a subtree from the plot, click on the left-most node that you want removed. From the pop-up menu, select "Exclude subtree."

  7. Highlight a subtree

    Highlighting a subtree Subtree highlighted
    Highlighting a subtree
     To highlight a subtree, click on the root node of that subtree and select "Highlight subtree" from the menu. Only one subtree may be highlighted at a time.

    If the node is already highlighted, you will instead have the option of un-highlighting the subtree.

  8. Reroot the tree

    Rerooting the tree Tree rerooted
    Rerooting the tree
     A subtree can be set as a new outgroup from the root. Click on the root node of that subtree and select "Reroot" from the menu. The tree will be redrawn with the subtree branching from the root.

  9. Swap node branches

    Swapping branches Branches swapped
    Swapping upper and lower branches
     Swapping the upper and lower branches of a node can be done by clicking on that node and selecting "Swap branches" from the menu.

    This can be used to manually group taxa by kingdom.

  10. View intron presence probability

    Viewing intron history Intron history plot
    Looking at intron presence probability
     Intron presence probabilities at ancestral nodes can be displayed in the tree as pie charts if the NEXUS data file contains a "History" block.

    First, make sure the intron data is displayed. Click the "H" under the appropriate intron label and select "View probability pie chart" from the menu. Red indicates probability of presence for the selected intron at each node.

    A file with this data can be found here.