From Gene Trees to Species Trees through a Supertree Approach

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.