During my PhD I initiated and wrote the Agora ancestral-genome reconstruction toolkit. Although I was not using any version control system, I was still making regular backups of my workspace. This repository links those snapshots and give a little bit of history about this project.
The final product is available in another repository: https://github.com/DyogenIBENS/Agora/ , and the reconstructions are released on the Genomicus browser http://www.genomicus.biologie.ens.fr/genomicus/