Building species trees from larger parts of phylogenomic databases

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. First of all, we propose to separately preprocess MUL trees in order to remove their redundant parts with respect to speciation events. For this purpose, we present a tree isomorphism algorithm for MUL trees that can be applied to the pairs of subtrees hanging from duplication nodes. This preprocess lowers the number of duplication nodes in gene trees....

• Type: Journal
• Year: 2011
• Where: IANDC
• Authors: Celine Scornavacca, Vincent Berry, Vincent Ranwez
• Keywords: Gene Trees, IANDC 2011, MUL Tree, Tree