kmer {kmer}

Fast K-mer Counting and Clustering for Biological Sequence Analysis.

Description

The kmer package contains tools for rapidly computing distance matrices, building large trees, and clustering operational taxonomic units using fast alignment-free k-mer counting and divisive clustering techniques.

Functions

A breif description of the primary kmer functions are provided with links to their help pages below.

K-mer counting

• kcount counts all k-letter words in a sequence or set of sequences using a sliding window of length k

Distance matrix computation

• kdistance calculates pairwise distances between sequences based on k-mer counts

• mbed embeds sequences as vectors of k-mer distances to a set of seed' sequences

Alignment-free clustering

• cluster builds a phylogenetic tree by successively splitting a set of sequences (recursive partitioning) based on k-mer counts

• otu heirarchically clusters a set of sequences until a predefined furthest neighbor dissimilarity threshold is reached.