Software


Ultrametric Trees
This Excel spreadsheet randomly generates a distance matrix for an ultrametric tree containing up to 20 taxa. Working in small groups, students can reconstruct the tree using pencil and paper. We recommend using 6-8 taxa to introduce students to phylogenetic concepts and methods.

Additive Trees
An elaboration of "Ultrametric Trees", this Excel spreadsheet randomly generates a distance matrix for an additive tree containing up to 20 taxa. Relaxation of the ultrametric criterion adds an extra challenge for students who have mastered the simpler case.

Split Decomposition
This Excel spreadsheet constructs a four-taxa unrooted bifurcating tree, using either randomly generated or user-input topology and branchlengths. It then calculates split indices for each of the three possible trees to assess the support for each. This program emphasizes the distinction between building a tree (i.e., framing a phylogenetic hypothesis) and testing one.

Growth Models
This Excel spreadsheet compares user-input growth data with predictions under linear, exponential, and logistic models of growth. Students can input parameters for each model; the program graphs the results and computes a crude goodness-of-fit measure. Introduces concepts of modeling and statistical analysis that can be more thoroughly explored using standard statistics software (JMP, SAS, etc.) From the "Modeling More Mold" activity in Microbes Count! .

SIR Model

This Excel spreadsheet implements an SIR (Susceptible/Infected/Resistant) model of epidemiology for vector-borne diseases. Up to three microbial strains with different virulence and transmission parameters can be modeled and the results graphed. Originally designed to explore coevolution of myxoma and rabbits, the model is easily generalized to other systems. From the "Plague on Both Houses" activity in Microbes Count! .

[last updated July 2003]