Abstract
Phylogenetic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) method to find the distances between the sequences which is a parameter independent measure. We used DNA sequences from Candida species and phylogenetic trees were obtained using un-weighted pair-group with arithmetic mean method. We used three reduced alphabets for the DNA sequences which were clustered by taking into account different physico-chemical properties of DNA. RCM gives as good results as the distance determination method and among the physico-chemical properties, Keto/Amino grouping is found to give the most accurate tree which is topologically closest to the desired phylogeny.
Highlights
DNA sequencing methodology has become one of the most widely used techniques in molecular biology and DNA sequences submitted to databases has increased exponentially each year, resulting in an enormous increase in the size and amount of data generated[1]
Phylogenetic analysis of molecular sequences is indispensible in the areas of Systematic and Evolutionary Biology and DNA sequences are important resources for phylogenetic analysis
We propose to compare effects of physico-chemical features of DNA on phylogeny construction by Relative Complexity Measure (RCM) method using three reduced alphabets
Summary
DNA sequencing methodology has become one of the most widely used techniques in molecular biology and DNA sequences submitted to databases has increased exponentially each year, resulting in an enormous increase in the size and amount of data generated[1]. Phylogenetic analysis of molecular sequences is indispensible in the areas of Systematic and Evolutionary Biology and DNA sequences are important resources for phylogenetic analysis. It is becoming a very common procedure to analyze relationships within a taxonomic group by isolating sequenced DNA and constructing the phylogeny. Methods for constructing phylogenies have been developed by the discipline of Phylogenetics or Cladistics[2]. Most of the methods are based on multiple alignment of DNA sequences and calculation of distances (proportional to insertions, deletions and mutations) between these sequences. Once the distance matrix is obtained, one can choose the appropriate clustering method to obtain the phylogenetic tree
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