Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due
to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple
alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a
growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The “distances” used
in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first
review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic
analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view.
Keywords: Alignment-free method, dissimilarity, distance, genome, phylogenetic analysis.
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