DyogenIBENS/Agora ? reverse-engineered prompt

Build me a Python tool for ancestral genome reconstruction called AGORA.

It should take a species tree, gene lists for each species, and either gene trees or orthology group files, then reconstruct ancestral gene order and produce ancestral genome files that can be used for downstream comparative genomics. I want it to have a simple command line workflow, with one basic mode for standard runs and another mode for more fragmented ancestral genomes. Please include the sample inputs and outputs in a way that makes it easy to test with the example data, and make sure the setup instructions work with either a conda environment or pip install.

Also add a clear integrity check script or command that verifies everything is installed correctly and can generate ancestral genomes in a temporary folder. If you need to, look up the current docs online so the implementation matches the intended usage and file formats.