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 (GRoupin

SUBMITTER: Dalevi D 

PROVIDER: S-EPMC2228325 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature