title: Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.
abstract: BACKGROUND
  Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence database. Hierarchical group names are typically manually assigned in trees, an approach that becomes unfeasible for very large topologies.
  
  
  RESULTS
  We have developed an automated iterative procedure for delineating stable (monophyletic) hierarchical groups to large (or small) trees and naming those groups according to a set of sequentially applied rules. In addition, we have created an associated ungrouping tool for removing existing groups that do not meet user-defined criteria (such as monophyly). The procedure is implemented in a program called GRUNT (GRouping, Ungrouping, Naming Tool) and has been applied to the current release of the Greengenes (Hugenholtz) 16S rRNA gene taxonomy comprising more than 130,000 taxa.
  
  
  CONCLUSIONS
  GRUNT will facilitate researchers requiring comprehensive hierarchical grouping of large tree topologies in, for example, database curation, microarray design and pangenome assignments. The application is available at the greengenes website 1.
authors.affiliation: Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720,USA. DDalevi@lbl.gov
authors.forename: Daniel
authors.initials: D
authors.lastname: Dalevi
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: Desantis
authors.forename: Jakob
authors.initials: J
authors.lastname: Fredslund
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
mesh_terms: D000465:Algorithms; D002965:Classification; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S