Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Methodology article

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

Yasin Bakış1*, Hasan H Otu23, Nivart Taşçı4, Cem Meydan5, Neş’e Bilgin4, Sırrı Yüzbaşıoğlu6 and O Uğur Sezerman5

Author affiliations

1 Department of Biology, Abant İzzet Baysal University, Bolu, 14280, Turkey

2 Department of Medicine, BIDMC Genomics Center, Harvard Medical School, Boston, MA, 02115, USA

3 İstanbul Bilgi University, Department of Genetics and Bioengineering, Eyüp, İstanbul, 34060, Turkey

4 Department of Molecular Biology and Genetics, Boğaziçi University, Bebek, İstanbul, 34342, Turkey

5 Biological Sciences and Bioengineering, Sabancı University, Tuzla, İstanbul, 34956, Turkey

6 Department of Botany, İstanbul University, Süleymaniye, İstanbul, 34460, Turkey

For all author emails, please log on.

Citation and License

BMC Bioinformatics 2013, 14:20  doi:10.1186/1471-2105-14-20

Published: 17 January 2013

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.

Keywords:
Resampling; Alignment free; Phylogenetics; Relative Complexity Measure; Galanthus