Course materials

GeneBridge: Inferring the Evolutionary Rooting of Orthologous Genes

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The course "GeneBridge: Inferring the Evolutionary Rooting of Orthologous Genes" is 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.

DOI: https://doi.org/10.5281/zenodo.17533991

Licence: Creative Commons Attribution Share Alike 4.0 International

Contact: https://dalmolingroup.imd.ufrn.br/contact/

Keywords: orthology, Evolutionary bioinformatics, Systems biology

Target audience: Researchers, Graduate students, Biologists, Bioinformaticians

Resource type: Course materials

Version: v1.0

Status: Active

Prerequisites:

  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.

Learning objectives:

  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]

Date created: 2024-11-07

Date modified: 2025-11-05

Authors: Dalmolin Systems Biology Group

Scientific topics: Evolutionary biology, Systems biology

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