Besides this the MITOS Galaxy tool can be installed in any Galaxy (for instance, any of the national usegalaxy instances which may provide more resources for you).
One big advantage of the Galaxy platform is that it integrates a wide variety of bioinformatics
tools. Interesting for mitochondrial data are for instance getorganelle, mitobim, and plasmidspades.
If you want to learn more about Galaxy check out the
Galaxy training network,
The Galaxy community help forum, or
The Galaxy community hub.
The command line option is only suggested for power users with experience with Linux.
Background: Why the MITOS service can't be provided as a web-service anymore:
The current implementation of the webserver had serious security issues
The webserver part of MITOS needs to be ported to python 3
Maintenance of the webserver consumed quite a bit of time
M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, P. F. Stadler MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation
Molecular Phylogenetics and Evolution 2013, 69(2):313-319 link