This lesson is part of the workshop “Using the Open Tree of Life for your Research”, SSB 2020.
Prerequisites
Background in systematics and phylogenetics. Some experience with the R programming language.
This lesson is part of the workshop “Using the Open Tree of Life for your Research”, SSB 2020.
Prerequisites
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.