OverviewΒΆ

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/

  • Source code: 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

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.