phytools: phylogenetic tools in R development page

This page contains the source code for all the functions in the phytools R package. Although some functions will work when loaded directly from source, many have hidden internal dependencies. Consequently, I would encourage interested users to download and install phytools and its dependent packages. If you have questions about using these functions please don't hesitate to contact me: liam.revell@umb.edu. In fact, if you find any problems, errors, or bugs in phytools, or if you have suggestions about how they might be improved, please send me an email or post a comment to my development blog. Thanks!

Please check out the article describing phytools here. This article should be cited if the phytools package or any of the functions of this page (including modifications thereof) are used in publication. Click here for a list of prior citations of phytools.

Quick link: index and help pages of all functions in the current CRAN version of phytools.

Package versions

All of the following package versions should be considered beta as I am constantly updating, expanding, and fixing bugs in phytools. For source code of the most recent "minor" (i.e. non-CRAN) phytools build, click here and select the most recent version. Feedback welcome.

Latest major phytools release (minor releases):

Older major phytools versions (minor versions):

CRAN:

Package installation

CRAN installation: For R in Mac OS or Linux, or for R>=2.13 in Windows to install phytools from CRAN simply type:
> install.packages("phytools")
and then select a repository.

Windows installation: Navigate to the directory containing the binary file, and, substituting version # for a.b-c, type:
> install.packages("phytools_a.b-c.zip",repos=NULL)

Installation from source (Mac OS, Linux, Unix, Windows):
> install.packages("phytools_a.b-c.tar.gz",repos=NULL,type="source")

(**Note - to install from source you will first need to install a gcc compiler such as MinGW or Xcode. This is not difficult. For more information, search the web or send me an email.)

Source files in phytools

My contact information is as follows:

Liam J. Revell
University of Massachusetts, Boston
100 Morrissey Blvd., Boston MA 02127
Wheatley Hall W-03-15
email: liam.revell@umb.edu




webpage  development blog
Last modified December 15 2014.