GeneBridge: Inferring the Evolutionary Rooting of Orthologous Genes

Author

Dalmolin Systems Biology Group

1 Lesson overview

đź”’ License: Creative Commons Attribution Share Alike 4.0 International License

đź‘Ą Target Audience: Researchers, graduate students, and biologists interested in evolutionary analysis.

📶 Level: Intermediate

⬅️ Prerequisites To be able to follow this course, learners should have knowledge in:

  1. Basic knowledge of the R programming language (loading libraries, handling data frames).
  2. Familiarity with fundamental concepts in evolutionary biology (e.g., genes, orthologs, phylogenetic trees).
  3. Being comfortable working with RStudio or a similar R environment.

📖 Description This repository contains the materials for the course “GeneBridge: Inferring the Evolutionary Rooting of Orthologous Genes,” organized by Dalmolin’s Systems Biology Group, based at the Bioinformatics Multidisciplinary Environment (BioME) at UFRN. This workshop is divided into three parts: (1) Performing the Rooting Analysis, (2) Plotting Rooted Genes, and (3) Plotting Abundances.

➡️ Learning Outcomes: By the end of the course, learners will be able to:

  1. Understand the theoretical basis of evolutionary rooting and the Bridge algorithm. [Understanding]
  2. Apply the GeneBridge package to infer the evolutionary root for a set of orthologous genes. [Applying]
  3. Analyze and interpret the output tables and rooting results. [Analysing]
  4. Create and customize plots to visualize rooted genes on a phylogenetic tree. [Creating]
  5. Generate and evaluate plots of gene abundances across different clades. [Evaluating]

⌛ Time estimation: 180 minutes

⚙️ Requirements: Participants must have a laptop with a recent version of R and RStudio installed. Specific R package dependencies (e.g., GeneBridge) are detailed in the repository’s setup instructions.

🙏 Acknowledgements:

  • Bioinformatics Multidisciplinary Environment (BioME - IMD/UFRN)
  • Postgraduate Program in Bioinformatics (PPg-Bioinfo - UFRN)