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

Yasin Bakiş, Hasan H. Otu, Nivart Taşçi, Cem Meydan, Neş'e Bilgin, Sirri Yüzbaşioǧlu, O. Uǧur Sezerman

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: 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.

Original languageEnglish (US)
Article number20
JournalBMC bioinformatics
Volume14
Issue number1
DOIs
StatePublished - Jan 17 2013

Fingerprint

Galanthus
Complexity Measure
Phylogeny
Phylogenetic Tree
Robust Methods
Alignment
Robustness
Testing
Chloroplast DNA
Chloroplast
DNA
Nuclear RNA
Phylogenetic Analysis
Ribosomal RNA
DNA sequences
Turkey
Fungi
Mitochondrial DNA
rRNA Genes
DNA Sequence

Keywords

  • Alignment free
  • Galanthus
  • Phylogenetics
  • Relative Complexity Measure
  • Resampling

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. / Bakiş, Yasin; Otu, Hasan H.; Taşçi, Nivart; Meydan, Cem; Bilgin, Neş'e; Yüzbaşioǧlu, Sirri; Sezerman, O. Uǧur.

In: BMC bioinformatics, Vol. 14, No. 1, 20, 17.01.2013.

Research output: Contribution to journalArticle

Bakiş, Yasin ; Otu, Hasan H. ; Taşçi, Nivart ; Meydan, Cem ; Bilgin, Neş'e ; Yüzbaşioǧlu, Sirri ; Sezerman, O. Uǧur. / Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. In: BMC bioinformatics. 2013 ; Vol. 14, No. 1.
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