Essays on the Binary Representations of the DNA Data

Abstract

The advancement of modern genomics has led to the large-scale industrial production of molecular data and scientific outcomes. Simultaneously, conventional DNA character alignments (sequence alignments) are utilized for DNA-based phylogenetic analyses without further recoding procedures or any a priori determination of character polarity, contrary to the requirements of foundations of phylogenetic systematics. These factors are the primary reasons why the binary perspective has not been implemented in modern molecular phylogenetics. In this study, we demonstrate how to recode conventional DNA data into various types of binary matrices, either unpolarized or with established polarity. Despite its historical foundation, our analytical approach to DNA sequence data has not been adequately explored since the inception of the molecular age. Binary representations of conventional DNA alignments allow for the analysis of molecular data from a purely comparative or static perspective. Furthermore, we show that the binarization of DNA data possesses broad mathematical and cultural connotations, making them intriguing regardless of their applications to different phylogenetic procedures.

Keywords

• DNA
• binary characters
• character polarity
• phylogenetic systematics
• cladistics
• Leibniz