The phylogram R package is a tool for for developing phylogenetic trees as deeply-nested lists known as "dendrogram" objects. It provides functions for conversion between "dendrogram" and "phylo" class objects, as well as several tools for command-line tree manipulation and import/export via Newick parenthetic text. This improves accessibility to the comprehensive range of object-specific analytical and tree-visualization functions found across a wide array of bioinformatic R packages.
A brief description of the primary phylogram functions are provided with links to their help pages below.
read.dendrogram reads a Newick
parenthetic text string from a file or text connection
and creates an object of class "dendrogram"
write.dendrogram outputs an object of class
"dendrogram" to a text string or file in Newick
format
as.phylo.dendrogram converts a dendrogram to
an object of class "phylo"
"dendrogram"
as.dendrogram.phylo converts a "phylo" object
to a dendrogram
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)
as.cladogram modifies the "height" attributes of the
nodes such that all leaves terminate at zero