Statistically-Consistent k-mer Methods for Phylogenetic Tree Reconstruction

Statistically-Consistent k-mer Methods for Phylogenetic Tree Reconstruction
Elizabeth S. Allman, John A. Rhodes, Seth Sullivant

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.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s