title   
  

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

Bakış, Yasin and Otu, Hasan H. and Taşçı, Nivart and Meydan, Cem and Bilgin, Neşe and Yüzbaşıoğlu, Sırrı and Sezerman, Uğur (2013) Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure. BMC Bioinformatics, 14 . ISSN 1471-2105

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Official URL: http://dx.doi.org/10.1186/1471-2105-14-20

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.

Item Type:Article
Additional Information:Article Number: 20
Uncontrolled Keywords:Resampling; Alignment free; Phylogenetics; Relative Complexity Measure; Galanthus
Subjects:Q Science > Q Science (General)
ID Code:23433
Deposited By:Uğur Sezerman
Deposited On:14 Jan 2014 14:51
Last Modified:17 Oct 2014 14:33

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