Msktuple: An integrated R library for alignment-free multiple sequence k-tuple analysis

Abstract

Recently alignment-free sequence comparison methods based on promoter-frequency distance measures have gained popularity. This paper reports on the implementation and validation of several alignment-free sequence analysis methods for representing and quantifying between-sequence distances and sequence variability. The msktuple library includes the following sequence comparison techniques: locational k-tuple, naive k-tuple, CV-Tree, and their ensemble variants. These metrics are used to determine the dissimilarity between sequences using k-letter words. In support of open-science, we provide open-source software, R-scripts, and protocols implementing the new techniques. These tools will support collaboration, enable independent validation, promote result reproducibility and enable tool interoperability.