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This software is an add-on package for Mathematica(c) by Wolfram, Inc. that 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.
- Download the latest version of the package at https://github.com/pdpolly/Phylogenetics-for-Mathematica (right click on link to save as file)
- Open the file in Mathematica
- Under the File menu, choose “Install”
- Under Type of Item choose “Package”, under source choose the file you just saved, under Install Name choose a short name for the package (e.g., “PollyPhylogenetics”)
- Once installed, enter the command “<<PollyPhylogenetics`” to use the functions.
- Use the function PhylogeneticsVersion[] to determine which version you have installed.
Phylogenetics for Mathematica is documented in the PDF user guide that is located in the repository.
The package has functions for importing trees in Newick format; drawing trees; converting trees to tables with entries for each node that describe its ancestral node, the length of its subtending branch, and whether it is a tip or internal node; re-rooting trees; mapping continuous traits onto trees; estimating evolutionary rates and ancestor reconstructions for continuous traits; calculating phylogenetic statistics like Blomberg's Kappa, Pagel's lambda, and phylogenetic community statistics; performing phylogenetic least squares regression (PGLS) and calculating phylogenetic independent contrasts (PIC); simulating continuous traits on tress; and fitting evolutionary statistical models to time series such as found in stratigraphic succession in the paleontological record.
Polly, P.D. 2019. Phylogenetics for Mathematica. Version 6.5. https://github.com/pdpolly/Phylogenetics-for-Mathematica