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A tutorial on how to use MITOS, including an example and the used sample data, can be found here.
Feature types: PCG tRNA rRNA
OH OL intron
Circular:                          Use Al Arab et al.:       
E-value Exponent:
Maximum Overlap:
Fragment Quality Factor:
Standard Code:
Cutoff:
Clipping Factor:
Fragment Overlap:
Local only:
Sensitive only:
ncRNA overlap:
MITOS2 is now available on usegalaxy.eu.

Note that this is a beta version. We would be grateful for bug reports and comments.

Citation:
A Donath, F Jühling, M Al-Arab, SH Bernhart, F. Reinhardt, PF Stadler, M Middendorf, M Bernt
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
Nucleic Acids Research 2019, 47(20):10543–10552 link