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Reconstruction, analysis, and visualization of phylogenomic data with the ETE Toolkit

Date:

Tuesday, 1st September

Time:

17:00 - 20:00 (CEST)

Instructors 

  • Jaime Huerta Cepas | Centre for Plant Biotechnology and Genomics (CBGP), Spain
  • François Serra | Barcelona Supercomputing Center (BSC), Spain

Helpers 

  • Ziqi Deng | Centre for Plant Biotechnology and Genomics (CBGP), Spain
  • Ana Hernández-Plaza | Centre for Plant Biotechnology and Genomics (CBGP), Spain
  • Carlos Pérez Cantalapiedra | Centre for Plant Biotechnology and Genomics (CBGP), Spain
  • Álvaro Rodríguez del Río | Centre for Plant Biotechnology and Genomics (CBGP), Spain

Summary

Phylogenomic analysis is a key step in a wide range of genomic and metagenomic studies. Its applications go from reconstructing species relationships or studying the evolution of gene families, to delineating new species from metagenomic samples, detecting horizontal gene transfer events, predicting orthology and annotating gene function, characterizing duplication events, and dating the emergence of specific gene functions. Automating phylogenomic analysis, however, requires the development of bioinformatic workflows and ad-hoc scripts to process and analyze large volumes of complex data.

In this tutorial, we will introduce ETE Toolkit, a Python framework that assists in the programmatic reconstruction, analysis and visualization of phylogenetic trees and multiple sequence alignments. ETE provides both a comprehensive API to handle phylogenetic data and a collection of command-line tools to perform basic analyses in phylogenomics: running phylogenetic workflows, comparing trees, testing evolutionary hypotheses, dealing with taxonomy databases and visualizing results. Moreover, ETE offers programmatic visualization of phylogenetic trees and multiple sequence alignments, a unique feature that integrates well under the scientific software stack in Python (e.g. Jupyter Notebooks) and complements other general visualization frameworks such as Matplotlib, seaborn or plotly.

In this tutorial, we aim at providing a practical entry point to phylogenomic data analysis to any researcher interested in automating the reconstruction and analysis of phylogenetic trees, building their own analytical algorithms based on tree-like structures, or creating custom visualizations out of phylogenetic data.

Target audience

Any bioinformatician interested in automating the reconstruction and analysis of phylogenetic trees, building their own analytical algorithms based on tree-like structures, or creating custom visualizations out of phylogenetic data.

Maximum participants

Unlimited

Requirements

Intermediate level in Python programming and basic Shell. Ideally, participants should be fluent in basic Python scripting (e.g. creating functions, using basic operators, conditions and loops, handling lists, sets and dictionaries, understanding string operations, importing modules), and know basic Bash (e.g. navigate through directories, basic shell scripting in Bash, using shell pipes, grepping files, etc.). Participants should have ete3 and jupyter preinstalled in their computers.

Schedule

Time (CEST)
Details
17:00 - 17:35 Designing and running phylogenomic workflows using ete-build
17:35 - 18:00 Performing adaptation tests on phylogenetic trees with ete-evol
18:00 - 18:20 Comparing, annotating and visualizing (command line)
18:20 - 18:30 Break
18:30 - 18:45 Handling trees programmatically (ETE API Basics)
18:45 - 19:15 Programmatic handling of phylogenetic trees and alignments (ETE API)
19:15 - 20:00 Advance Tree Visualization