phyloDB: A framework for large-scale phylogenetic analysis of sequence based typing data

Abstract

PHYLODB is a modular and extensible framework for large-scale phylogenetic analyses of sequence based typing data, which are essential for understanding epidemics evolution. It relies on the Neo4j graph database for data storage and processing, providing a schema and an API for representing and querying phylogenetic data. Custom algorithms are also supported, allowing users to perform heavy computations directly over the data, and to store results in the database. Multiple computation results are stored as multilayer networks, promoting and facilitating comparative analyses, as well as avoiding unnecessary ab initio computations. The experimental evaluation results showcase that PHYLODB is efficient and scalable with respect to both API operations and algorithms execution.

Keywords

• Large scale phylogenetic analysis
• Phylogenetic inference
• Graph database