# Software

## Applets that I use in teaching

Developing these applets helped me understand concepts, and I hope they are useful to you as well.

### Phylogenetics

- Pagel’s lambda, delta, and kappa
- Ornstein-Uhlenbeck vs. Brownian Motion
- Dirichlet base frequency distribution
- Jukes-Cantor transition probabilities
- Geometry of tree space

### Statistics

### Natural Selection

- Natural selection ball-drop game
- Biston betularia (1848-1898)
- Biston betularia (1959-2003)
- Selective Sweep

### Population Genetics

## C++ Bayesian phylogenetics software tutorial

This is a tutorial showing how to create a functioning Bayesian phylogenetics application in C++. It makes use of the BeagleLib library for computing likelihoods, and illustrates how to implement data partitioning, heated chains, rate heterogeneity, codon models, polytomy-friendly tree topology priors, and steppingstone marginal likelihood estimation.

## MCMC Robot

This is a free app for iPad/iPhone that illustrates the basic principles of Markov chain Monte Carlo using the metaphor of a robot following simple rules to walk around on a landscape and, in the process, learning about the topography of the landscape. For the iOS version, P. Lewis acknowledges the support provided by NSF grant DEB-1036448 (GrAToL).

A D3 javascript version of MCMC Robot that can be run inside any modern web browser is also available (MCMC Robot).

Note: an older Windows version of this app is available below or from the MCMC Robot home page.

## Galax

Program that estimates topological information content from a tree file (or list of tree files) representing a sample from the posterior distribution generated by a Bayesian phylogenetic analysis. The analysis performed by Galax is described in the following manuscript:

Lewis, P. O., M.-H. Chen, L. Kuo, L. A. Lewis, K. Fučíková, S. Neupane, Y.-B. Wang, and D. Shi. 2016. Estimating Bayesian phylogenetic information content. Systematic Biology 65(6):1009-1023.

Important! The methods outlined in the above paper and implemented in the Galax software are most useful for problems involving fewer than 12 taxa. Please give Table 2 in the paper your full attention before using the software on your own data, especially if you suspect information content is low. We are working on a more general solution that will more accurately measure information content.

Download Galax v1.0.0

## GDA

Program by Paul O. Lewis and Dmitri Zaykin designed to accompany the book “Genetic Data Analysis” by Bruce S. Weir (1996, Sinaur Associates). Computes linkage and Hardy-Weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.

Reference:

Weir, B. S. 1996. Genetic Data Analysis. 2nd ed. Sinauer Associates, Sunderland, Massachusetts. 376 pages.