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Distance-based phylogenetic inference from typing data: a unifying view

2020Journal article Restricted access
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dc.contributor.authorVaz, Cátia
dc.contributor.authorNascimento, Marta
dc.contributor.authorCarrico, Joao
dc.contributor.authorRocher, Tatiana
dc.contributor.authorFrancisco, Alexandre P.
dc.date.accessioned2021-05-10T10:17:03Z
dc.date.available2021-05-10T10:17:03Z
dc.date.issued2020
dc.description.abstractTyping methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. Moreover, their use is becoming standard, in particular with the introduction of high-throughput sequencing. On the other hand, the data being generated are massive and many algorithms have been proposed for a phylogenetic analysis of typing data, addressing both correctness and scalability issues. Most of the distance-based algorithms for inferring phylogenetic trees follow the closest pair joining scheme. This is one of the approaches used in hierarchical clustering. Moreover, although phylogenetic inference algorithms may seem rather different, the main difference among them resides on how one defines cluster proximity and on which optimization criterion is used. Both cluster proximity and optimization criteria rely often on a model of evolution. In this work, we review, and we provide a unified view of these algorithms. This is an important step not only to better understand such algorithms but also to identify possible computational bottlenecks and improvements, important to deal with large data sets.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationVAZ, Cátia; [et al] – Distance-based phylogenetic inference from typing data: a unifying view. Briefings in Bioinformatics. eISSN 1477-4054. Vol. 00, N.º 0 (2020), pp. 1-16pt_PT
dc.identifier.doi10.1093/bib/bbaa147pt_PT
dc.identifier.eissn1477-4054
dc.identifier.urihttp://hdl.handle.net/10400.21/13314
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherOxford Academicpt_PT
dc.relationPTDC/CCI-BIO/29676/2017 - FCTpt_PT
dc.relationTUBITAK/0004/2014 - FCTpt_PT
dc.relationCMUP-ERI/TIC/0046/2014 - FCTpt_PT
dc.relationSAICTPAC/0021/2015 - FCTpt_PT
dc.relationUIDB/50021/2020 - FCTpt_PT
dc.relation.publisherversionhttps://watermark.silverchair.com/bbaa147.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAq4wggKqBgkqhkiG9w0BBwagggKbMIIClwIBADCCApAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMoeQCexfm1EuQceR1AgEQgIICYQQEwQ-5UG6KuWxa-PE-TeTtsDR5APw_WluzM5dmA7HI2_DXL9Ir979Nl9nVttb3YbVeKrvUHjpBVvtaXLLlBWMl9nzUJN12cQVJa8hhYVdwB65RkZ5QD_zsXTOmCXIrsbNKgLc6rKjDk0256VgI4nF_XLiaCn78KqW1eQ9-smTb8SvNdfkgRbFkED3aaTjYiEuDhoCMCK54vUvWV3Mh8iQia6wZrAwhtpQ-hVHh9kV8uZNGXdOK9enVGAgIziCA4UgbrjUhQCk0foOy_gsCAFshW249CHF7_KmMlsszthUtfjDWRTr8zymlSjpAazL5fNl8G_lzDDIyOoRBBiyfE97SxiPKzf4KkewI_xAiXbHI2-j17JXPRwZ6KlAsUOlRWOhOBXLG2DcoA7PdZRTcTU98fXLfR5IJLBCFkKjksAiioTUQOoC5H0cWoz5izL_hQZ_skipqyH37Tqavc5-JwCRIemHUQDuydvTW0ZRIItr5nK9QZ3vdYHRguJuL2S8IG9UFRIyulps7NM-yRpsZ5hUaq5oHWq5Ror5H6BJNxLABJMfXhtxhogA_lZD_cwabOkY6pVW0-r97ZsBDQBhOeCedy_LvFtfWk5dyGOKMUnW8Yzv6rersajyXkrM-q4tCAA__dgI2IZGlqnmwy_w7VQBjkczodQ_C0dgced9SHWFk0uPPvml2UqRPjM5cT8aBxfHDMHA9dq8wU2bvfdYUQBkkwnQyAhJHAeAsK0pPvGFGW47Nx0eWrw9yGHgUeZzdxfDuRy8EBPwN009DYRfhopfNxwE5ObVWnZhLKq6AIm6EXQpt_PT
dc.subjectPhylogenetic inferencept_PT
dc.subjectClustering methodspt_PT
dc.subjectTree search algorithmspt_PT
dc.titleDistance-based phylogenetic inference from typing data: a unifying viewpt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage16pt_PT
oaire.citation.issue0pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titleBriefings in Bioinformaticspt_PT
oaire.citation.volume00pt_PT
person.familyNameVaz
person.familyNameCarrico
person.givenNameCátia
person.givenNameJoao
person.identifier.ciencia-id8718-741E-BBD9
person.identifier.orcid0000-0001-6074-3074
person.identifier.orcid0000-0002-5274-2722
person.identifier.ridADC-1473-2022
person.identifier.ridA-7367-2008
person.identifier.scopus-author-id27267941600
person.identifier.scopus-author-id8266333200
rcaap.rightsclosedAccesspt_PT
rcaap.typearticlept_PT
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relation.isAuthorOfPublication5f4ad9ce-0a68-496f-a0d6-2062d39f4702
relation.isAuthorOfPublication.latestForDiscovery5f4ad9ce-0a68-496f-a0d6-2062d39f4702

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