Phylogenic 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) to find the distances between the sequences which is not a parameter dependent 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 physicochemical properties of DNA. RCM gives as good results as the distance determination method and among the physicochemical properties, Keto/Amino grouping is found to give the most accurate tree which is topological closest to the desired phylogeny.