Phylogenetics for Mathematica (Ver. 2.1)

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P. David Polly


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. The file is a ".m" file, 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.



Phylogenetics, Ancestral Node Reconstruction, Newick Trees


Polly, P. D. 2012. Phylogenetics for Mathematica. Version 2.1. Department of Geological Sciences, Indiana University: Bloomington, Indiana.


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