Using the Open Tree of Life for your Research -- with R!

This lesson was initially developed as part of the workshop “Using the Open Tree of Life for your Research”, at SSB 2020.


Background in systematics and phylogenetics. Some experience with the R programming language.


Setup Download files required for the lesson
00:00 1. Package version How do you know your installed package versions?
How do you instal a certain version of a package?
00:10 2. Finding your taxa in the Open Tree of Life Taxonomy What is the Open Tree of Life Taxonomy?
What are OTT ids?
What does TNRS stand for?
00:20 3. Getting a piece of the Synthetic Open Tree of Life What is the synthetic Open Tree of Life?
How do I interact with it?
Why is my taxon not in the tree?
00:30 4. Dealing with "broken" and "invalid" taxa What is a broken taxon?
How do I detect it?
00:40 5. Getting an induced subtree of all taxa within a taxonomic rank How do I get all taxa from a certain taxonomic rank?
00:50 6. Getting studies and trees supporting relationships in a synthetic subtree What are the original studies supporting relationships in my synthetic subtree?
01:00 7. Getting branch length information (proportional to time) for you taxa How do I find supporting trees that include branch lengths?
How do I subset them to include just the taxa I am interested in?
01:10 8. Summarizing branch length information How do I summarize information from different source chronograms?
How do I choose a preferred source chronogram?
01:20 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.