Querying phylogenies visually

Abstract

Querying and visualization of phylogenetic databases remain a great challenge due to their inherent complex structures. Popular phylogenetic databases such as Tree of Life and TreeBASE do not support flexible querying through query languages for the exploration of their contents. The query facility employed in these databases is usually limited to complex interfaces or is too limited to be useful for many applications. The most striking shortcoming of these systems is that they do not treat phylogenies (trees) as first citizens. In this paper, we introduce a novel visual query language for phylogenetic databases in which trees are recognized as basic units. We also introduce a Web based query interface, based on this language, for querying any tree like structure, either on the Web (e.g. Tree of Life), or in traditional relational databases (e.g. TreeBASE). As an aside, the mapping technique used in our system makes it possible to interoperate between a variety of heterogeneous phylogenetic databases. Finally, we demonstrate that the basic tree manipulation operators proposed in this paper can be used to form unlimited types of tree queries that were not possible in popular phylogenetic databases until now.