Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure

Basit Öğe Kaydı
dc.WoS.categoriesBiochemical Research Methods; Biotechnology & Applied Microbiology; Mathematical & Computational Biologyen_US
dc.authorid0000-0002-9253-8152en_US
dc.contributor.authorOtu, Hasan H.
dc.date.accessioned2021-02-25T08:47:14Z
dc.date.available2021-02-25T08:47:14Z
dc.date.issued2013-01-17
dc.description.abstractBackground: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees. Different parameter combinations chosen for the multiple alignment may result in different phylogenies. A new non-alignment based approach, Relative Complexity Measure (RCM), has been introduced to tackle this problem and proven to work in fungi and mitochondrial DNA. Result: In this work, we present an application of the RCM method to reconstruct robust phylogenetic trees using sequence data for genus Galanthus obtained from different regions in Turkey. Phylogenies have been analyzed using nuclear and chloroplast DNA sequences. Results showed that, the tree obtained from nuclear ribosomal RNA gene sequences was more robust, while the tree obtained from the chloroplast DNA showed a higher degree of variation. Conclusions: Phylogenies generated by Relative Complexity Measure were found to be robust and results of RCM were more reliable than the compared techniques. Particularly, to overcome MSA-based problems, RCM seems to be a reasonable way and a good alternative to MSA-based phylogenetic analysis. We believe our method will become a mainstream phylogeny construction method especially for the highly variable sequence families where the accuracy of the MSA heavily depends on the alignment parameters.en_US
dc.fullTextLevelFull Texten_US
dc.identifier.doi10.1186/1471-2105-14-20en_US
dc.identifier.issn1471-2105
dc.identifier.pmid23323678en_US
dc.identifier.scopus2-s2.0-84872263945en_US
dc.identifier.urihttps://hdl.handle.net/11411/3299
dc.identifier.urihttps://doi.org/10.1186/1471-2105-14-20
dc.identifier.wosWOS:000314580800001en_US
dc.identifier.wosqualityQ1en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.nationalInternationalen_US
dc.numberofauthors5+en_US
dc.publisherBmcen_US
dc.relation.ispartofBmc Bioinformaticsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectResamplingen_US
dc.subjectAlignment freeen_US
dc.subjectPhylogeneticsen_US
dc.subjectRelative Complexity Measureen_US
dc.subjectGalanthusen_US
dc.titleTesting robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measureen_US
dc.typeArticleen_US
dc.volume14en_US

Dosyalar

Orijinal paket
Listeleniyor 1 - 1 / 1
Küçük Resim
İsim:
Otu 2013.pdf
Boyut:
1.62 MB
Biçim:
Adobe Portable Document Format
Açıklama:
İndir
Lisans paketi
Listeleniyor 1 - 1 / 1
Küçük Resim Yok
İsim:
license.txt
Boyut:
1.71 KB
Biçim:
Item-specific license agreed upon to submission
Açıklama:
İndir

Koleksiyon

Faculty of Engineering and Natural Sciences
PubMed Indexed Publications
Scopus Indexed Publications
Web of Science Indexed Publications