aevol : http://www.aevol.fr
Aevol is a computational platform that allows for the study and manipulation of populations of digital organisms evolving under different conditions. Using Aevol simulations, one can better understand evolutionary forces and mechanisms leading to specific genome and transcriptome structures, as well as indirect selection pressures involved in the evolution of cooperation and genetic information transfer.
Treerecs : https://gitlab.inria.fr/Phylophile/Treerecs
Treerecs is an open-source (species- and gene-) tree reconciliation software. It can correct, rearrange and (re-)root gene trees with regard to a given species tree. It was designed to be both efficient and easy to install and to use.