Growing Phylogenetic Trees Using Hierarchical Clustering

Onno Eberhard

We compare mitochondrial DNA of different species to build a phylogenetic tree. The main challenge is that the calculation of the Levenshtein distance is very slow for large sequences. We introduce an approximate scheme which uses Levenshtein for lower-level details and a fast distance based on sequence length for high-level attributes. The tree is built using average linkage hierarchical clustering.

@article{eberhard-2022-growing,
  author = {Eberhard, Onno},
  title = {Growing Phylogenetic Trees Using Hierarchical Clustering},
  elocation-id = {2022.02.08.479565},
  year = {2022},
  doi = {10.1101/2022.02.08.479565},
  publisher = {Cold Spring Harbor Laboratory},
  url = {https://www.biorxiv.org/content/early/2022/02/10/2022.02.08.479565},
  eprint = {https://www.biorxiv.org/content/early/2022/02/10/2022.02.08.479565.full.pdf},
  journal = {bioRxiv}
}