An Assessment of PC-mer's Performance in Alignment-Free Phylogenetic Tree Construction

Abstract

Background: Sequence comparison is essential in bioinformatics, serving various purposes such as taxonomy, functional inference, and drug discovery. The traditional method of aligning sequences for comparison is time-consuming, especially with large datasets. To overcome this, alignment-free methods have emerged as an alternative approach, prioritizing comparison scores over alignment itself. These methods directly compare sequences without the need for alignment. However, accurately representing the relationships between sequences is a significant challenge in the design of these tools. Methods:One of the alignment-free comparison approaches utilizes the frequency of fixed-length substrings, known as K-mers, which serves as the foundation for many sequence comparison methods. However, a challenge arises in these methods when increasing the length of the substring (K), as it leads to an exponential growth in the number of possible states. In this work, we explore the PC-mer method, which utilizes a more limited set of words that experience slower growth 2^k instead of 4^k compared to K. We conducted a comparison of sequences and evaluated how the reduced input vector size influenced the performance of the PC-mer method. Results: For the evaluation, we selected the Clustal Omega method as our reference approach, alongside three alignment-free methods: kmacs, FFP, and alfpy (word count). These methods also leverage the frequency of K-mers. We applied all five methods to 9 datasets for comprehensive analysis. The results were compared using phylogenetic trees and metrics such as Robinson-Foulds and normalized quartet distance (nQD). Conclusion: Our findings indicate that, unlike reducing the input features in other alignment-independent methods, the PC-mer method exhibits competitive performance when compared to the aforementioned methods especially when input sequences are very varied.