Using the Open Tree of Life for your Research, R section

This lesson is part of the workshop “Using the Open Tree of Life for your Research”, SSB 2020.


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


Setup Download files required for the lesson
00:00 1. 1. Finding your taxa in the Open Tree of Life Taxonomy What is the Open Tree Taxonomy?
What are OTT ids?
What does TNRS stand for?
00:10 2. 2. 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?
00:20 3. 3. Dealing with "broken" and "invalid" taxa How do I detect a broken taxon?
00:30 4. 4. Getting an induced subtree of all taxa within a taxonomic rank How do I get all taxa from a certain rank?
00:40 5. 5. Getting studies and trees supporting relationships in a synthetic subtree What are the original studies supporting relationships in my synthetic subtree?
00:50 6. 6. 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?
01:00 7. 7. Summarizing branch length information How do I summarize information from different source chronograms?
How do I choose a preferred source chronogram?
01:10 Finish

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