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

2024-05Journal article Restricted access
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dc.contributor.authorLourenço, Bruno
dc.contributor.authorVaz, Cátia
dc.contributor.authorCoimbra, Miguel E.
dc.contributor.authorFrancisco, Alexandre P.
dc.date.accessioned2024-11-05T11:11:06Z
dc.date.available2024-11-05T11:11:06Z
dc.date.issued2024-05
dc.description.abstractPHYLODB 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.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationLourenço B, Vaz C, Coimbra ME, Francisco AP – phyloDB: A framework for large-scale phylogenetic analysis of sequence based typing data. SoftwareX 2024, 26; https://doi.org/10.1016/j.softx.2024.101668pt_PT
dc.identifier.doi10.1016/j.softx.2024.101668pt_PT
dc.identifier.issn2352-7110
dc.identifier.urihttp://hdl.handle.net/10400.21/17836
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherElsevierpt_PT
dc.relationInstituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa
dc.relation.publisherversionhttps://www.sciencedirect.com/science/article/pii/S2352711024000396?via%3Dihubpt_PT
dc.subjectLarge scale phylogenetic analysispt_PT
dc.subjectPhylogenetic inferencept_PT
dc.subjectGraph databasept_PT
dc.titlephyloDB: a framework for large-scale phylogenetic analysis of sequence based typing datapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleInstituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F50021%2F2020/PT
oaire.citation.endPage6pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleSoftwareXpt_PT
oaire.citation.volume26pt_PT
oaire.fundingStream6817 - DCRRNI ID
person.familyNameVaz
person.familyNameCoimbra
person.givenNameCátia
person.givenNameMiguel
person.identifier.ciencia-id8718-741E-BBD9
person.identifier.ciencia-id0F17-A236-551B
person.identifier.orcid0000-0001-6074-3074
person.identifier.orcid0000-0002-7191-5895
person.identifier.ridADC-1473-2022
person.identifier.scopus-author-id27267941600
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsclosedAccesspt_PT
rcaap.typearticlept_PT
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relation.isAuthorOfPublicationce60af86-1102-48b4-87ad-9ba24a5cc3cf
relation.isAuthorOfPublication.latestForDiscovery0c5cb0fd-7cd7-4a16-86a8-7a68188e53ff
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