Overview
========

FREEDA (Finder of Rapidly Evolving Exons in Diverse Assemblies) is a Python built end-to-end
automated pipeline to detect positive selection, created for experimental cell biologists 
without training in computational biology and molecular evolution. 

- Documentation: `https://ddudka9.github.io/freeda/ <https://ddudka9.github.io/freeda/>`_
- Source code: `https://github.com/DDudka9/freeda <https://github.com/DDudka9/freeda>`_
- Requirements:
	- Operating systems compatible:
		- MacOS: Mojave, Big Sur, Monterrey and Ventura (Apple Silicon must have Rosetta installed)
		- Linux Ubuntu 22.04 LTS
		- Windows (currently through VirtualBox only)
	- Disc space:
		- min 100 GB per taxon e.g. primates (we recommend using a hard drive with 500GB space)
	- Stable Internet connection
- (NEW) You can now run FREEDA using a web-based server Tamarind Bio `https://www.tamarind.bio/freeda <https://www.tamarind.bio/freeda>`_
	

If you use FREEDA for published work, please cite the original paper:

Dudka D, Akins RB, Lampson MA. FREEDA: An automated computational pipeline guides experimental testing of protein innovation. J Cell Biol. 2023 Sep 4;222(9):e202212084. doi: 10.1083/jcb.202212084. Epub 2023 Jun 26. PMID: 37358475; PMCID: PMC10292211.

FREEDA is published under the GPLv3 license.