Description Functions K-mer counting Distance matrix computation Alignment-free clustering
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.
A breif description of the primary kmer functions are provided with links to their help pages below.
kcount
counts all k-letter words in a
sequence or set of sequences using a sliding window of
length k
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
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.
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