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An Alignment Free Framework for Taxonomic Inference From Codon and Codon-Pair Usage.

Sharon Yalov Handzel1, Brian Rikshpun1, Nigam Padhiar2

  • 1Department of Machine Learning and AI Afeka Tel-Aviv Academic College of Engineering Tel-Aviv Israel.

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|April 22, 2026
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Summary
This summary is machine-generated.

Alignment-free genomic data analysis uses codon usage profiles for taxonomic inference. Taxonomic Consistency (TC) validates predictions, showing codon usage offers coherent structure for rapid screening and evolutionary studies.

Keywords:
alignment‐freeclassificationclusteringcodon usagecodon‐pair usagemachine learningtaxonomy

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Alignment-free methods offer scalable solutions for analyzing large genomic datasets.
  • Taxonomic inference, phylogenetic quality control, and genomic data screening benefit from efficient analytical approaches.

Purpose of the Study:

  • To present a model-agnostic framework for genomic representation using codon and codon-pair usage profiles.
  • To introduce Taxonomic Consistency (TC) as an external index for evaluating taxonomic predictions and clustering.
  • To assess the impact of data handling strategies and feature types on taxonomic inference performance.

Main Methods:

  • Genome representation using 64-dimensional codon usage and 4096-dimensional codon-pair usage profiles.
  • Development and application of Taxonomic Consistency (TC) for external validation against hierarchical taxonomy.
  • Assessment of supervised models and unsupervised clustering using internal (Silhouette) and external (TC) validation metrics.

Main Results:

  • Handling class imbalance and principled normalization significantly improved performance over sequence-level preprocessing.
  • Codon usage profiles achieved the highest TC and demonstrated coherent unsupervised structure.
  • Codon-pair features provided complementary resolution within specific taxonomic clades.

Conclusions:

  • Alignment-free codon and codon-pair representations offer a practical complement to traditional tree-based methods.
  • Taxonomic Consistency (TC) provides transparent external validation for ecological and evolutionary analyses.
  • The framework facilitates rapid genomic screening, sanity checks, and exploratory analyses, particularly at higher taxonomic ranks.