Software
All of my public code is available on GitHub. I also maintain several software projects, including:
- Homebrew package manager for macOS and Linux, maintainer, Project Leadership Committee
- Brewsci biology software packaging for Homebrew
- Fish Tree of Life website, for viewing data on ray-finned fish taxonomy and phylogeny
- fishtree R package, interface to the fishtreeoflife.org website
- TACT: Taxonomy Addition for Complete Trees stochastic polytomy resolver
If you found my software useful, please consider supporting my work with a cocktail 🍸.
I’ve written extensively on software and code on my blog. Several of my published manuscripts also describe software:
(2019) J Chang, DL Rabosky, ME Alfaro. Estimating diversification rates on incompletely sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology 69(3):602-611 doi:10.1093/sysbio/syz081 [link]
(2019) J Chang, DL Rabosky, SA Smith, ME Alfaro. An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life. Methods in Ecology and Evolution 10(7):1118-1124 doi:10.1111/2041-210X.13182
(2018) DL Rabosky, J Chang, PO Title, PF Cowman, L Sallan, M Friedman, K Kaschner, C Garilao, TJ Near, M Coll, ME Alfaro. An inverse latitudinal gradient in speciation rate for marine fishes. Nature 559(7714):392-395 doi:10.1038/s41586-018-0273-1
(2015) J Chang, ME Alfaro. 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
(2013) DL Rabosky, F Santini, JM Eastman, SA Smith, BL Sidlauskas, J Chang, ME Alfaro. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications 4:1958 doi:10.1038/ncomms2958
(2012) BC Faircloth, J Chang, ME Alfaro. TAPIR enables high-throughput estimation and comparison of phylogenetic informativeness incorporating locus-specific substitution models. [arXiv:1202.1215]