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ETE10 Analysis and manipulation of phylogenomic data using ETE |
| Course Timetable |
| Wed, June 23rd |
Day #1
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| 09:30 - 11:00 |
1. Introduction to phylogenomics
1.1 General phylogenetic pipeline 1.2 Phylogenomics: scope and applications 1.3 Dealing with large collections of trees: Phylomes |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 | 1.4 Public phylogenomic resources: PhylomeDB, Ensembl Compara, TreeFam
1.5 Orthology and Paralogy prediction based on phylogenetic analysis 2. Installing ETE 2.1 Using ETE libraries 2.2 Interactive ETE sessions using ipython |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 |
3. Tree basics
3.1 Reading and writing trees 3.2 Rooting, pruning, splitting and concatenating trees 3.3 Browsing tree topology: performing per node operations 3.4 Searching nodes by their attributes 3.5 Basic tree visualization: the ETE GUI |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 |
4. Comparing tree topologies:
4.1 Linking to the the Phylip package: consensus & treedist programs 4.2 Comparing tree topologies using Treeko 5. Tree annotation 5.1 Adding extra information to the tree nodes 5.2 Using the extended newick format 5.3 Using the PhyloXML format |
| Thu, June 24th |
Day #2
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| 09:30 - 11:00 |
6.Building clustering trees and phylogenetic profiles
6.1 Linking trees to numeric profiles and matrices 6.2 Using profiles as node properties 6.3 Visualizing trees with profiles: tree heatmaps and profiling plots |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 |
7.Dealing with phylogenetic trees
7.1 Associating nodes with multiple sequence alignments 7.2 Species aware trees 7.2.1 Species guided rooting 7.2.2 Checking for monophyletic clades |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 |
7.3 Detecting orthology and paralogy relationships
7.3.1 Tree reconciliation 7.3.2 The species overlap algorithm 7.3.3 Working with speciation and duplication events |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 |
7.3 Dating duplication events
7.5 Working with Species trees: 7.5.1 Using NCBI taxonomy tree |
| Fri, June 25th |
Day #3
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| 09:30 - 11:00 |
8.Programmatic tree visualization: creating custom tree pictures
8.1 Understanding ETE's language: Styles, Faces and Layouts 8.2 Creating custom layout functions 8.3 Modifying colors and general tree aspect (styles) |
| 11:00 - 11:30 | Coffee Break |
| 11:30 - 12:30 |
8.4 Adding graphical information to nodes (faces)
8.4.1 External image faces 8.4.2 Text based faces 8.4.3 Profile faces 8.5 Rendering trees as PNG or PDF images |
| 12:30 - 14:00 | Lunch Break |
| 14:00 - 16:00 |
9. Exploiting public phylogenomic resources
9.1. The PhylomeDB API (working with complete phylomes) 9.2. Working with Ensembl Compara trees 9.2.1 Reading Ensembl annotated trees |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 |
10. Advanced topics:
10.1 Creating custom image faces 10.2 Interoperability with other toolkits 10.3 Extending ETE 10.4 Your specific requests |
| Course Homepage |
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Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: April 23rd 2010 |