Alternative splicing is a ubiquitous process in eukaryotes, which allows the production of distinct transcripts from the same gene by joining different combinations of exons. It has raised interest in the last few decades because of its significant role in gene diversification, as well as in cancer. The study of the evolution of transcripts across a set of homologous genes provides additional information on gene evolution, such as the identification of conserved isoforms, the history of isoform gains and losses along gene phylogenies, and the evolution of alternative splicing.
In this talk, I will present a unified view of transcript phylogeny reconstruction problems, and I will describe current challenges and existing solutions, including a set of methods and a database we have developed to study transcript evolution.