This add-in package for Mathematica performs basic phylogenetic functions, including reading and drawing Newick format trees, calculating phylogenetically independent contrasts, reconstructing ancestral values for continuous traits, performing random walks, and simulating continuous traits on phylogenetic trees.
Installation. Download the binary file from the latest release. The file is in Mathematica's ".m" format, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line <<PollyPhylogenetics`, using either this suggested name or another.
Latest user guide: https://github.com/pdpolly/Phylogenetics-for-Mathematica/releases/download/v.6.9/Guide.to.PollyPhylogenetics.6.9.pdf
Funding for development for this package has been provided by grants NSF EAR 1338298, the Robert R. Shrock fund at Indiana University, the Yale Institute for Biospheric Studies, and the Lilly Endowment through its support for the Indiana University Pervasive Technology Institute and the Indiana METACyt Initiative.
Cite as: Polly, P.D. 2023. Phylogenetics for Mathematica. Version 6.9. https://github.com/pdpolly/Phylogenetics-for-Mathematica
