Article In: dblp, scopus, orcid
phyloDB: A framework for large-scale phylogenetic analysis of sequence based typing data
SoftwareX
— 2024 — Elsevier B.V.
Key information
Authors:
Published in
February 22, 2024
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.
Publication details
Authors in the community:
Bruno Miguel Leandro Lourenço
ist193973
Cátia Raquel Jesus Vaz
ist45098
Miguel E. Coimbra
ist162460
A P Francisco
ist14152
Publication version
VoR - Version of Record
Publisher
Elsevier B.V.
Link to the publisher's version
https://www.sciencedirect.com/science/article/pii/S2352711024000396?via%3Dihub
Title of the publication container
SoftwareX
First page or article number
101668
Last page
101668
Volume
26
ISSN
2352-7110
WoS (Web of Science)
Fields of Science and Technology (FOS)
computer-and-information-sciences - Computer and information sciences
Keywords
- Large scale phylogenetic analysis
- Phylogenetic inference
- Graph database
Publication language (ISO code)
eng - English
Rights type:
Open access
Creative Commons license
CC-BY-NC - Attribution-NonCommercial
Financing entity
OLISSIPO Project
Title of the project, award or grant: OLISSIPO – Fostering Computational Biology Research and Innovation in Lisbon
Funding Stream: Horizon 2020 research and innovation programme – Twinning / Widening participation (H2020-WIDESPREAD)
Identifier for the funding entity: https://doi.org/10.13039/501100000780
Type of identifier of the funding entity: Crossref Funder
Number for the project, award or grant: 951970
Financing entity
Fundação para a Ciência e a Tecnologia
Title of the project, award or grant: INESC-ID R&D Unit – Base Funding (UIDB/50021/2020)
Funding Stream: FCT R&D Units Multi-annual Funding programme
Identifier for the funding entity: https://doi.org/10.13039/501100001871
Type of identifier of the funding entity: Crossref Funder
Number for the project, award or grant: UIDB/50021/2020