Toni Gabaldon leads the Comparative Genomics group at the Centre for Genomic Regulation. and is Associate Professor at the Universitat Pompeu Fabra. He got his PhD on comparative genomics  at the "Radboud Universiteit Nijmegen" (The Netherlands) in 2005. His group has made significant contributions to the development of tools for phylogenomic analysis including, phylomeDB [2], ETE [3]. TreeKo, trimAl ,and  MetaPhOrs, as well as in the exploitation of phylogenomic data for the understanding of the evolution and function of complex biological processes. Gabaldon has extensive experience in teaching bioinformatics and molecular evolution at the undergraduate and graduate levels.

homepage: http://big.crg.cat/people/toni_gabaldon

Jaime Huerta-Cepas is a postdoc researcher within the Comparative Genomics group at the Centre for Genomic Regulation. He got his PhD on human genome evolution [1] and large scale phylogentic analyses at the "Universidad Autónoma de Madrid" in 2008. Jaime is the main developer of the phylomeDB database [2], and the ETE toolkit [3]. His work focuses on applying large scale phylogenetic analyses to address different biological problems, such as understanding gene duplication, the evolution of gene expression, functional genome annotation, orthology and paralogy prediction, and the reconstruction of species Tree of Life. Personal homepage: http://jhcepas.cgenomics.org

Marina Marcet-Houben obtained her degree in Biochemistry in the Rovira i Virgili University (Tarragona, Spain). She did her PhD on fungal phylogenomics in the Comparative Genomics lab at the Center for Genomic Regulation in Barcelona. Her main research interests are related to the use of large scale phylogenomics tools to study the evolution of fungi [4] as well as in studies involving the robustness of species trees [5]. Marina is an active collaborator in the phylomeDB project and the main developer of TreeKo, a tool for comparing phylogenetic tree topologies.

• 1 Lectures: Introduction to phylogenomics
• 1.1 General phylogenetic pipeline
• 1.2 Phylogenomics: scope and applications
• 2. ETE basics (brief introduction)
•  
• 2.1 Installing ETE
• 2.2 Using ETE libraries
• 2.3 Interactive ETE sessions using ipython
• 2.4 Tree basics

• 3. Basic Tree operations (examples and exercises)
• 3.1 Reading and writing trees
• 3.2 Creating trees from scratch
• 3.3 Browsing tree topology: performing per node operations
• 3.4 Searching nodes by their attributes
• 3.5 Modifying trees
• 3.6 Rooting, pruning, splitting and concatenating trees

• 4. Tree Annotation ( brief introduction)

(examples and exercises)

• 4.1 Adding extra information to the tree nodes
• 4.2 Exporting data using  the extended newick format
• 4.3 Exploring trees attributes using the GUI

• 5. Lectures:  orthology and paralogy
• 6. Phylogenetic trees in ETE (brief introduction)

(examples and exercises)

• 6.1 Associating nodes with multiple sequence alignments
• 6.2 Species aware trees
• 6.3 Species guided rooting
• 6.4 Detecting monophyletic clades
• 6.3 Detecting orthology and paralogy relationships
• 6.3.1 Tree reconciliation 
• 6.3.2 The species overlap algorithm
• 6.3.3 Working with speciation and duplication events
• 6.4 Relative dating duplication events

• 7 Comparing tree topologies: (introduction and exercises)
• 7.1 Phylip package: consensus & treedist programs
• 7.2 Comparing tree topologies using Treeko

• 8.Building clustering trees and phylogenetic profiles(brief introducction)

(examples)

• 8.1 Linking trees to numeric profiles and matrices
• 8.2 Using profiles as node properties
• 8.3 Visualizing trees with profiles: tree heatmaps and profiling plots
/ul>

GLOBAL EXERSICE : Functional annotation of the newly sequenced genome of Pea Aphid

• 9. Lectures:  Dealing with large collections of trees: Phylomes
• 9.1 Public phylogenomic resources: PhylomeDB, Ensembl Compara, TreeFam
• 10. PhylomeDB API (brief introduction)

• 11 The programmable tree drawing engine
• 11.1 Controlling node aspect (NodeStyle)
• 11.2 Adding graphical information to nodes (Faces)
• 11.2.1 Types of NodeFaces
• 11.2.2 NodeFace properties
• 11.2.2 NodeFace placement
• 11.3 Dynamic control of image rendering (TreeStyle and layout functions)
• 11.4 Rendering trees as PNG, SVG or PDF images

• 12. Advanced topics
• 12.1 Webplugin (interactive tree images on the web)
• 12.2 Nexml and PhyloXML formats
• 12.3 Creating custom Node Faces

• 13 Course wrap up:
• 13.1 Comments on the exercises
• 13.2 Questions & requests