Construction of Phylogenetic Relationships Based on 8-mer Spectra Distribution Characteristics of Vertebrate Whole Genome Sequences
Zhenhua Yang, Li Wang, Guojun Liu, Dongsheng Yu, Xiangjun Cui · 2025
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Description
Zhenhua Yang and four co-authors build family trees of vertebrates from whole genomes without lining the genomes up, in this 2025 study. Comparing species by aligning their DNA is slow and fails for distant relatives. A shortcut counts short words of DNA, called k-mers: the pattern of which eight-letter words appear, and how often, carries an evolutionary fingerprint.
The team extracted features from the 8-letter spectra of genome subsets, finding that their distributions track species relationships closely. Their method combines two feature types: class-level features capturing broad patterns of separability and conservation, and order-level features from ranking the words. Together they reconstruct evolutionary relationships across vertebrates at genome scale. Fast, alignment-free trees could let researchers use the flood of new genomes for evolutionary questions that alignment-based methods cannot reach.
Catalog record
| CREATOR | Zhenhua Yang, Li Wang, Guojun Liu, Dongsheng Yu, Xiangjun Cui |
|---|---|
| YEAR | 2025 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 36 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |