All of my code is made available on GitHub. I’m also a maintainer for the Homebrew package manager, specifically for the science and Linux repositories.

I’ve also written extensively on software and code on my blog. Several of my published manuscripts also describe software:

Jonathan Chang, Michael E Alfaro. (2015). Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data. Methods in Ecology and Evolution 7(4):472-482 doi:10.1111/2041-210x.12508

Daniel L Rabosky, Francesco Santini, Jon M Eastman, Stephen A Smith, Brian L Sidlauskas, Jonathan Chang, Michael E Alfaro. (2013). Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4:1958 doi:10.1038/ncomms2958

Brant C Faircloth, Jonathan Chang, Michael Alfaro. (2012). TAPIR enables high-throughput estimation and comparison of phylogenetic informativeness incorporating locus-specific substitution models. arXiv:1202.1215