title: Simplifying gene trees for easier comprehension.
abstract: 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 tree to a "cartoon tree" created manually, we note that both agree to a high degree.
  
  
  CONCLUSIONS
  Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families. The software is available at http://www.uni-muenster.de/Bioinformatics/services/treesim/.
authors.affiliation: Division of Bioinformatics, Biology Department, University Münster, Schlossplatz 4, 48149 Münster, Germany. mail@pluti.de
authors.forename: Paul-Ludwig
authors.initials: PL
authors.lastname: Lott
authors.forename: Marvin
authors.initials: M
authors.lastname: Mundry
authors.forename: Christoph
authors.initials: C
authors.lastname: Sassenberg
authors.forename: Stefan
authors.initials: S
authors.lastname: Lorkowski
authors.forename: Georg
authors.initials: G
authors.lastname: Fuellen
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D019143:Evolution, Molecular; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins