Phylogenetics for Mathematica (Ver. 2.1)

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Date

2012-07-24

Journal Title

Journal ISSN

Volume Title

Publisher

P. David Polly

Abstract

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.

Description

Keywords

Phylogenetics, Ancestral Node Reconstruction, Newick Trees

Citation

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

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You are free: to Share — to copy, distribute and transmit the work to Remix — to adapt the work Under the following conditions: Attribution — You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Noncommercial — You may not use this work for commercial purposes. Share Alike — If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one. With the understanding that: Waiver — Any of the above conditions can be waived if you get permission from the copyright holder. Public Domain — Where the work or any of its elements is in the public domain under applicable law, that status is in no way affected by the license. Other Rights — In no way are any of the following rights affected by the license: Your fair dealing or fair use rights, or other applicable copyright exceptions and limitations; The author's moral rights; Rights other persons may have either in the work itself or in how the work is used, such as publicity or privacy rights.

Type

Software