Simplifying gene trees for easier comprehension

Background: In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important. Results: We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tre...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Paul-Ludwig Lott, Marvin Mundry, Christoph Sassenberg, Stefan Lorkowski, Georg Fuellen
• Keywords: BMCBI 2006, Gene Trees, Simplification, Tree