Standardized Phylogenetic Evolutionary Analysis based on an Alignment Free Sequence Comparison Technique

Abstract

Phylogenetic analysis explains how species evolved throughout time. Multiple sequence alignments of proteins or genomes can be used to infer a phylogenetic tree. Understanding evolution requires phylogenetics, or reconstructing organisms' evolutionary relationships. The alignment of complete gene sequences of higher eukaryotes, as well as the construction of phylogenetic trees on the basis of these alignments, is a computationally costly and ambitious undertaking. To get around these restrictions, we compared the genomes of the Brassicales clade using alignment-free technique. A Chaos Representation (CR) can be evaluated for each nucleotide sequence, which depicts each nucleotide as a point in a square specified by the four nucleotides as nodes. As a result, every CR is a distinct fingerprint of the basic sequence. Each grid square in the CRs represents the presence of oligonucleotides of a given size in the sequence if the CRs are categorized by grid lines (Frequency Chaos Representation, FCR). To build phylogenetic trees of Brassicales species, we used distance metrics between FCRs.