This is a copy of the supplemental material from "Adaptive Radiation in Resource Competition in Digital Organisms" by Chow, Wilke, Ofria, Lenski, and Adami, published in Science (2004)
I am the "Chow" in the author list, and wrote the clustering source code. The source code of the version of Avida used in our experiments is included as part of the supplemental material, but I am not its author. For the newest version of Avida, find it on github or check out its website. Contact me for a copy of the journal article if you need it as well.
The clustering algorithm uses as a distance measure the number of steps separating one organism from another on the phylogenetic tree; since the digital organisms are initialized as a clonal population, this is straightforward to calculate.
The original README file for the supplementary material, slightly re-formatted for readability, follows:
Source code in source/
The Avida source code (version 1.99) used in the experiments is available in the source/avida/ directory.
The clustering source code is in the source/clustering directory.
Experimental Setup in exp-setup/
The experiment configuration files, sorted by experiment, are in the exp-setup/ directory. The config/ subdirectory of each experiment contains the files required by avida. The run_list file is a script to run the experiments on the Beowulf cluster at the Center for Microbial Ecology at Michigan State University.
The experiments:
calibration/
experiments to calibrate the cutoff used by the species clustering algorithm
resources/
limited resource environment experiments
resources_long_runs/
limited resource environment experiments with inflows of 10 and 0.1, with doubled duration to look at long term trends
freq_dependent_selection/
frequency dependent selection species invasion experiments -- one species from an ecosystem tries to invade a population of the other species in the ecosystem
ecosystem_invasion/
invasion experiments -- specialists from inflow 100000 replicates are competed against an ecosystem evolved at inflow 1000