From Gene Trees to Species Trees through a Supertree Approach

Abstract. Gene trees are leaf-labeled trees inferred from molecular sequences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species. Inferring a species tree from a set of multi-labeled gene trees (MUL trees) is a wellknown problem in computational biology. We propose a novel approach to tackle this problem, mainly to transform a collection of MUL trees into a collection of evolutionary trees, each containing single copies of labels. To that aim, we provide several algorithmic building stones and describe how they fit within a general species tree inference process. Most algorithms have a linear-time complexity, except for an FPT algorithm proposed for a problem that we show to be intractable. Key words: Computational biology, evolutionary trees, graphs and graph transformation, duplications, polynomial and FPT algorithms, intractability proof.

• Type: Conference
• Year: 2009
• Where: LATA
• Authors: Celine Scornavacca, Vincent Berry, Vincent Ranwez
• Keywords: Automata Theory, Evolutionary Trees, Gene Trees, LATA 2009, MUL Trees