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TreeDyn Hands on 1

TreeDyn Hands on 1. The purpose of this first hands on TreeDyn is simply to show very simply current operations you are probably familiar with using an other tree manipulation program such as njplot for example. In this document you will learn : How to open a newick file

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TreeDyn Hands on 1

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  1. TreeDyn Hands on 1 • The purpose of this first hands on TreeDyn is simply to show very simply current operations you are probably familiar with using an other tree manipulation program such as njplot for example. • In this document you will learn : • How to open a newick file • How to change the root of a tree • How to swap clusters • How to resize a tree • How to search for leaves containing a series of characters • How to label these leaves in a particular color • How to label terminal branches of these leaves with a particular color • How to save and print your work

  2. Open a file, newick format Drop down menu File Choose Open Select your file with the file selector Clic on "Open" (ouvrir in french)

  3. Resize the window to fit your needs Treedyn automatically sizes the tree so that labels can be read (figure below). You can first resize the window, as shown on the right

  4. Fit tree to window Next, right clic on the tree to open a dialog window Choose Navigation, Fit to window But see "note" next slide ! This produces the tree on the right. Now we want to choose a different root and swap some groups First, choose the proper panel (red arrow)

  5. Important note When you right clic on a tree to obtain a panel menu to deal with the tree, you may obtain a panel mennu as shown on the right ! Its color is yellow indicating that you have opened a panel menu general to treedyn, not restricted to the tree you are using. Close this panel and right clic on the tree itself, not on the window outside of the tree. We will study this yellow panel later on.

  6. Resizing a tree TreeDyn contains a series of tools for tree resizing. They are grouped in the panel indicated by the red arrow, which allows to select the different tools as shown in the red box. When the mouse pass over a tool, a pop up help appears. In this example, we will select the tool shown by the mouse arrow and resize the previous tree to the following : This was obtained with Shift-clic several times on the tree. Not very confortable for reading the leaves labels, but perhaps more convenient for rooting and branch swapping...

  7. Next choose the tools to re-root Select the branch leading to the outgroup chosen, the arrow turns into a hand, clic on the branch The root is now located in a different place. Lets swap two clusters

  8. This time, we choose the first tool of this panel Select a particular internal branch Clic on it, the two clusters defined by this internal branch are interchanged.

  9. Search for a leaf or a set of leaves. DropDown menu View, Select Find Panel as shown below This open the Find panel as shown on the right This panel allows to locate where a particular leaf is in the tree. In this exemple, every leaf label is listed as indicated (red) Simply double clic on a label to higlight the leaf (in red by default)

  10. Search for one leaf I have double clicked on 1300 By default, if you double click on an other leaf label, the previous highlights disappear (by default) and the second one is identified (red by default)

  11. Search for several leaves Search for every leaf whose label starts with 13 : enter 13* in the find box Hit Enter. All such leaves are now in red (by default). Note that *9 also works,as well as 1?3 and 9*8 !!! Now, we may wish to use a different color than red. From the drop down menu View, select "Parameters Panel". As shown on the right. This opens the color selector Choose a different color, either by clicking on the proper color (top) or by dragging the black dot to the proper place (red arrow) Now I have selected blue.

  12. Going back to the Find panel and looking for 13* will now turned these leaves in blue Good enough, but we want to conduct several searches, and have the result of each search in a different color. In the find panel, if you clic on reset (see on the right), you can see that by default, the option "automatic reset" is selected. In fact when selected this option erase the result of the previous search before diplaying the next result. Inactivate the "automatic reset" Now if I search first for 13* and then for 98*, I obtain the result below

  13. Find panel, bouton Reset, Reset (as shown below) remove all highlights. Search again for 98*, this labels leaves in blue Open the color panel choose green : Find leaves whose label starts with 13 : The two find operations have their respective colors.

  14. Highlights other features in a tree In the find panel, hit the "operation button as shown below, and select for example "Node Foreground Color" Use of the find panel as before, produces the following Finally you can combined different colors and operations.

  15. Save and export Use drop down menu File, Save or Save as to save the tree with its conformation and colors in internal treedyn format. Use drop down menu File, Export to export in many formats, including ps for making pdf file and various image formats Below is an excerpt of a tree saved as jpeg and opened with paint in windows. Finally, there is a print to print directly to your printer or producea ps or pdf file.

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