Data conversion tools for the Avida Digital Evolution Platform

Avida is a digital evolution platform in which self-replicating computer programs (digital organisms) compete, mutate, and evolve. Find the Avida software platform here or on GitHub. Read more about Avida in (Ofria and Wilke, 2004) or (Ofria et al., 2009).

This repository contains tools for converting from default Avida output formats to the ALife standard data formats.

Example Data

Find some example Avida data and the converted standard form of that data in ./example_data/. The .spop files are Avida population files (default Avida output files). They contain details about the genotypes in the current Avida population (extant genotypes) and details about the ancestral genotypes (going all the way back to the original population/organism) for all extant genotypes.

Phylogeny/Lineage Converter

At the moment, there's only a Python implementation available.

Python

The phylogeny (and lineage) data conversion tool can be found in ./avida_converters/phylogeny.py.

Usage

./avida_converters/phylogeny.py can be used as either a stand-alone script or be imported into your own python script.

Stand-alone usage:

usage: phylogeny.py [-h] [-output OUTPUT] [-format FORMAT] [-minimal]
                    [-list_formats]
                    input

Avida .spop to ALife standard-compliant phylogeny converter.

positional arguments:
  input                 Input avida .spop file.

optional arguments:
  -h, --help            show this help message and exit
  -output OUTPUT, -out OUTPUT
                        Name to assign to standard-compliant output file.
  -format FORMAT        What standard file format should this script output?
                        Valid options: ['csv', 'json']
  -minimal              Store minimal data in output file.
  -list_formats, -lsf   List available output formats.

References

Ofria, C., & Wilke, C. O. (2004). Avida: A Software Platform for Research in Computational Evolutionary Biology. Artificial Life, 10(2), 191–229. https://doi.org/10.1162/106454604773563612

Ofria, C., Bryson, D. M., & Wilke, C. O. (2009). Avida: A software platform for research in computational evolutionary biology. In Artificial Life Models in Software (Vol. 10, pp. 3–35). London: Springer London. https://doi.org/10.1007/978-1-84882-285-6_1