Jukes-Cantor Correction for Phylogenetic Tree Reconstruction
Emunefe, F. G.; Ugbene, I. J.
Show abstract
Phylogenetic tree reconstruction relies on accurate estimation of evolutionary distances between sequences. However, the observed Hamming distance between sequences can be misleading due to saturation, where multiple substitutions at the same site obscure the true evolutionary history. The Jukes-Cantor correction method addresses this by accounting for multiple substitutions, providing a more accurate representation of evolutionary distance. This study investigates the application of the Jukes-Cantor correction to the Hamming distance of genetic sequences in a case study, highlighting its impact on phylogenetic tree reconstruction. Our results demonstrate that the Jukes-Cantor correction significantly improves the accuracy of phylogenetic inference, particularly for sequences with substantial evolutionary divergence. However, the models reliance on simplifying assumptions, such as equal substitution rates and lack of base composition bias, limits its applicability to sequences with moderate levels of divergence. This study stands as a bedrock for further research into more complex models that can account for model violations and provide more accurate estimations of evolutionary distances for highly divergent sequences.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Evaluating the Number of Different Genomes in a Metagenome by Means of the Compositional Spectra Approach 94%
- Variant Evolution Graph: Can We Infer How SARS-CoV-2 Variants are Evolving? 94%
- A Weighted Network Analysis Framework for the Hourglass Effect - and its Application in the C. Elegans Connectome 93%
Similar papers in this journal
Similar papers in this journal
- AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers. 93%
- Insertions and deletions as phylogenetic signal in alignment-free sequence comparison 93%
- An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes 93%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.