Tools

Open-source software developed for detecting positive selection, quantifying centromere intensities, and analyzing satellite DNA shape.

Software

All tools are open-source and freely available. Each card links to documentation on this site, plus the source code repository on GitHub.

Molecular evolution

FREEDA

Finder of Rapidly Evolving Exons in Diverse Assemblies. A Python-built end-to-end automated pipeline to detect positive selection, designed for experimental cell biologists without training in computational biology. GUI-based; runs on MacOS and Linux (Windows via VirtualBox).

Documentation →   GitHub

Image analysis

Centrocalc

Automated 3D centromere quantification. Python tool to quantify centromere intensities from confocal immunofluorescence z-stacks. Segments centromere area, isolates spots via difference-of-Gaussians, and exports per-cell intensities and ImageJ ROIs.

Documentation →   GitHub

Genomics

DNA-shape

Satellite DNA shape quantification. Python scripts that compute the number of contiguous A/T stretches and tetranucleotides associated with narrow minor grooves in mouse major and minor satellite arrays from long-read assemblies.

Documentation →   GitHub

Citing

If you use any of these tools in published work, please cite the relevant paper. The FREEDA paper (Dudka, Akins, Lampson · J. Cell Biol. 2023) describes both FREEDA and the development of Centrocalc. The DNA-shape scripts accompany Dudka et al. · Nature 2025. Full citations are on the Publications page.

Map of Lehigh University in Bethlehem, PA with distances to nearby cities
Department of Biological Sciences
Iacocca Hall, 111 Research Drive
Bethlehem, PA 18015
Aerial view of Lehigh University's Mountaintop campus above the Lehigh Valley