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Thephylogram R package is a tool for for developingphylogenetic 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 treemanipulation and import/export via Newick parenthetic text.This improves accessibility to the comprehensive range of object-specificanalytical and tree-visualization functions found across a wide array ofbioinformatic R packages.

To downloadphylogram from CRAN and load the package, run

install.packages("phylogram")library("phylogram")

To download the latest development version from GitHub, run:

devtools::install_github("ropensci/phylogram",build_vignettes=TRUE) library("phylogram")

Consider the simple example of a tree with three members named"A", "B" and "C", where "B" and "C" are more closely relatedto eachother than they are to "A".An unweighted Newick string for this tree would be "(A,(B,C));".This text can be imported as adendrogram object using theread.dendrogram functionas follows:

library("phylogram")newick<-"(A,(B,C));"x<- read.dendrogram(text=newick)plot(x)

The following command writes the object back to the console inNewick format without edge weights:

write.dendrogram(x,edges=FALSE)

The syntax is similar when reading and writing text files,except that thetext argument is replaced byfile and avalid file path is passed to the function.

To convert the dendrogram to a "phylo" object, run

y<- as.phylo(x)

These and more examples are available in the package vignette.To view the vignette, runvignette("phylogram-vignette") or access itdirectly fromCRAN.

An overview of the package with links to the function documentation can be found by running

?phylogram

If you experience a problem using this package pleaseeither raise it as an issue onGitHubor post it on thephylogramgoogle group.

This software was developed atVictoria University of Wellingtonwith funding from a Rutherford Foundation Postdoctoral Research Fellowshipaward from the Royal Society of New Zealand.