How do I modify the results correctly when I use mitos2 on the Galaxy platform to annotate the mitochondrial genome? Some of the genes automatically calculated by the Galaxy platform are incorrect.
Welcome, @Liulu
The annotation comes directly from the underlying tool, so however those original developers created the algorithm is how it works. 
The authors have a webpage here with resources → http://mitos.bioinf.uni-leipzig.de/help.py
And the Galaxy tool form happens to have an extended Help section describing different usage of the tool’s parameters.
These are annotation predictions, so testing out different parameter combinations is how to potentially improve your results.
You could also review publications that do something similar to see if there are any known scientific factors for your specific genome to consider. The two publications listed on the form would be the base line references but there is probably discussion online in various scientific forums.
Citations
Donath, A., Jühling, F., Al-Arab, M., Bernhart, S. H., Reinhardt, F., Stadler, P. F., Middendorf, M., & Bernt, M. (2019). Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Research, 47(20), 10543–10552. https://doi.org/10.1093/nar/gkz833
Arab, M. A., zu Siederdissen, C. H., Tout, K., Sahyoun, A. H., Stadler, P. F., & Bernt, M. (2017). Accurate annotation of protein-coding genes in mitochondrial genomes. Molecular Phylogenetics and Evolution, 106, 209–216. https://doi.org/10.1016/j.ympev.2016.09.024
If you need help translating a direct usage to the Galaxy usage, you can share the external reference and a sample of your data for context and we can try to help more.
Hope this helps!
Thank you very much! 
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