Creating timetrees

Arbor has a few tools to create time-scaled phylogenetic trees. You can rescale your tree using standard methods like pathd8, penalized likelihood, or other methods that have been implemented in R. Alternatively, you can use our new tree rescaling method, described below, that calibrates a tree using dates from timetree.

Using Arbor to rescale your tree

In this example, we will obtain a tree from open tree of life and rescale it using dates from timetree of life.

We start with a list of taxa, testTaxa.csv. You can upload that csv file to your arbor instance, or just find it stored in the “treeTimer” collection.


Now, choose and run the function called “Match taxa to the timetree of life” from the treeTimer collection.


Use the following settings for this function:


When the function has stopped running, you should see a success message:


You can see a plot of the output by choosing the right settings in the Visualization tab.


Here is your timetree: