2015/11/05 by Elizabeth S. Allman, Allman, Elizabeth S., John A. Rhodes +3
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #92D15 #Evolution and Paleontology Studies #FOS: Biological sciences #Fractal and DNA sequence analysis #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.1511.01956
openalex publication_date 2015/11/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Frequencies of k-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between k-mer vectors to approximate a tree metric can be statistically inconsistent. To remedy this, we derive model-based distance corrections for orthologous sequences without gaps, which lead to consistent tree inference. The identifiability of model parameters from k-mer frequencies is also studied. Finally, we report simulations showing the corrected distance out-performs many other k-mer methods, even when sequences are generated with an insertion and deletion process. These results have implications for multiple sequence alignment as well, since k-mer methods are usually the first step in constructing a guide tree for such algorithms.