This program is a computer model that simulates evolution of a finite population of unicellular organisms.
To run it, you need Java Runtime Environment >= 7.
Models, simulation results, charts and backups reside in MODELS directory
To run models:
model.bat {model name without .properties} [rng seed as number] [property=value] [property=value]...
or ./model.sh under UNIX.
for example, model.bat monoploid 12345 steps=1500
It will produce {model-with-seed-and-properties}.txt with simulation results as well as printing steps on stdout.
It will also produce {model-with-seed-and-properties}.png with average fitness chart.
See default.properties in MODELS for a range of model parameters. Create your own *.properties files to override defaults.
You can put multiple properties files in subdirectory under MODELS. model.bat {subdir} will simulate them one by one.
Combining charts:
merge.bat [generations as number] {model-with-seed-and-properties} {another-model,yet-other-model...} {output}
or ./merge.sh under UNIX
Will read .txt files from MODELS and produce {output}.png in MODELS with multiple charts.
You can provide generations #, only those will be drawn. Otherwise it's longest output + some padding.
for example:
merge.bat 650 average-monoploid diploid,diploid-inexact triploid,triploid-inexact ploidy
Will produce a chart with 650 steps of average monoploid, two diploids in similar colors (red), two triploid in similar colors (green).
If you are using derivatives of this program, please don't hesitate to cite our paper:
Markov A, Kaznacheev IS. Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis. Biology Direct. 2016
http://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0131-8
For development, you need Maven. mvn package will compile source, run some tests, download dependencies and package compiled files.
Use mvn dependency:copy-dependencies and mvn license:update-project-license for maintenance.
There's also a branch named svg-charts that can produce vector SVG charts instead of PNG.