This repository contains the notebooks and scripts (or in some cases, sample scripts) for the "Annotation matters: the effect of structural gene annotation on orthology" paper. There are also README files within subdirectories to help with the analyses.

• In OMApre-processing you can find scripts that will help with the previous steps to running OMA
• In download, there are scripts to download the assemblies and proteomes used in our analysis
• In OMA, you can find sample scripts to run OMA
• In OrthoFinder, there are sample scripts to run OF
• In Augustusscripts, the scripts we used to run this software
• In GffCompare, scripts to process gffs prior to running GffCompare as well as scripts to run it
• In Trees, newick tree files used in the jupyter notebooks
• In GSpTDBenchmark, instructions and complementary scripts to run the Generalised Species Tree Discordance Benchmark, for which you will also need the git repo: https://github.com/qfo/benchmark-webservice.git
• In analysesnotebooks, the Jupyter Notebooks (python) used to produce our results and figures
• In Tables, output and input tables for the Jupyter Notebooks

If any issues arise, contact silvia.prietobanos@unil.ch