A graph theoretic approach to estimate gene family histories

The evolution of gene families involves duplications, losses, and transfers of genes to other organisms. To represent this history, a gene tree is embedded in a species tree, which creates homology relations between genes. Despite its key role in assigning functions to novel discovered genes, estimating gene family histories (GFHs) is still challenging, and several methods have been developed to address it. In particular, tree-free methods aim to infer homologous relationships between genes using sequence similarity without prior knowledge of the underlying trees. A novel approach based on graph theory falls into this category, and it has been partially implemented in a pipeline. In this presentation, I will give an overview of the family of graphs used in the pipeline, along with preliminary results and future directions.