The phylogram package contains functions for importing and exporting dendrogram objects in the Newick parenthetic text format, as well as several functions for command-line tree manipulation. With an emphasis on speed and computational efficiency, the package also includes a suite of tools for rapidly computing distance matrices and building large trees using fast alignment-free k-mer counting and divisive clustering techniques.
A breif description of the primary phylogram functions are provided with links to their help pages below.
read.dendrogram is a text parser that converts
parenthetic text (Newick strings) into objects of class
"dendrogram"
write.dendrogram outputs an object of class
"dendrogram" to a text string or file in Newick/New Hampshire
format
kcount tabulates all of the
k-letter words in a sequence or set of sequence
kdistance calculates pairwise
distances between sequences by k-mer counting
mbed embeds sequences as vectors of distances to a set of
'seed' sequences
topdown builds a phylogenetic tree by successively
splitting a set of sequences (recursive partitioning)
prune remove branches from a dendrogram object
based on regular expression pattern matching
ladder reorders the branches of a dendrogram
object to aid visualization
remidpoint recursively sets "midpoint" and "members"
attributes for a nested list/dendrogram object
reposition shifts a dendrogram object up or
down (or sideways if plotted horizontally)
ultrametricize modifies the "height" attributes of the
nodes such that all leaves terminate at zero