Schedule
Event local time
As shown in the schedule below, the course will cover a number of topics, which will be accompanied by daily assignments. These tasks will form part of a main exercise that will demonstrate the application of the learned skills and their use in the context of a comparative genomics and phylogenomics project, designed to replicate real analyses carried out in the field. The exact schedule of each day's lessons will be decided based on the organization and the needs (for example, transportation) of the final list of attendees.
| Date |
Time |
Topics |
| Monday (April 21th 2025) |
afternoon |
- Intro to the ETE toolkit Python library:
- Structure, philosophy and main modules
- Brief intro to Phylogenetics and Phylogenomics
- Running phylogenetic workflows with ETE Toolkit
- Loading and manipulating trees programmatically (Rooting, pruning, searching, printing, etc)
- Basic tree visualization
- PhyloCloud, an online platform to make sense of phylogenomic data
|
| Tuesday (April 22th 2025) |
full day
|
- Orthology prediction using ETE
- Detecting speciation and duplication events in gene trees
- Inferring pairwise orthology assignments (programmatically)
- Functional annotations → transferring data between orthologs
|
| Wednesday (April 23th 2025) |
full day |
- Tree annotation and phylogenetic profiling
- Adding custom properties to tree nodes
- TreeProfiler, binding trees and data tables
- Automated taxonomic annotations
- Inferring names, lineages and last common ancestors based on NCBI and GTDB databases
- Comparing and searching in trees
- Calculating distances between trees
- Searching patterns within trees
|
| Thursday (April 24th 2025) |
full day |
- Programmatic tree Visualization
- The new ETE v4.0 rendering engine: online, interactive visualization of large trees: advanced features
- Creating your own custom visualizations: faces, layouts, styles
- Exporting and sharing your visualization
|
| Friday (April 25th 2025) |
full day |
Finishing and reviewing the Main Exercise.
|
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