PAUP* communication package for Mesquite

David Maddison & Wayne Maddison

January 2001, version 0.9.

• Overview
• Modules
• Installation
• Examples
• Citation
• Acknowledgments

Overview

This package provides interaction with PAUP* (Swofford). It is currently only functional on Macintosh operating systems.

Modules

Some of the modules currently included are:

• DecayIndexPAUP -- Asks PAUP to do searches to find the length of the most parsimonious trees without each branch on the tree.
• LikelihoodFromPAUP -- Asks PAUP to calculate the likelihood of a tree.
• GammaFromPAUP -- Asks PAUP to estimate the gamma shape parameter for a tree using maximum likelihood.
• PInvarFromPAUP -- Asks PAUP to estimate the proportion of invariant characters in a Proportion Invariant Rates Model for a tree using maximum likelihood.
• tRatioFromPAUP -- Asks PAUP to estimate the transition/transversion ratio for a tree using maximum likelihood.

Installation

To install the PAUP* communications package, the "paupcomm" directory must be installed in the "mesquite" directory within "Mesquite Folder". This also requires the "comm" directory being present in the "mesquite" directory.

Examples

[Under construction]

Citation

[Under construction]

Acknowledgments

[Under construction]

© David Maddison & Wayne Maddison, 2001