Guanliang MENG

Hi Abhijit, basically, many genes will be missing, as plant mitogenomes have different gene content compared to animal mitogenomes. For example, the rRNA CM models and tRNA profiles were trained...

Hi Timz0605, Thanks for reporting the issue. I will check the program later, I don't know if there are bugs. And yes, you can also try `Arthropoda` or `Chordata` for...

Hi, MitoZ will output any sequences with more than 5 PCGs, see https://github.com/linzhi2013/MitoZ/wiki/FAQ#can-i-apply-mitoz-to-metagenomic-multiple-species-dataset for details. If you got two (or more) long mitogenomes, you can annotate them separately (`mitoz annotate`）.

I also added more description on the related wiki pages on this.

this file is only 3.6 Kb in size. It seems there are only a few mt sequences assembled. you may try to use smaller kmers?

Hi [dleopold](https://github.com/dleopold), Thank you very much for reporting the issue. I will check it when I have more time. I agree with your point "It would seem more appropriate to...

Could you please tell me the accessions for the "4 similar taxa"? thanks! I would like to check them further.

When I check this COX2 of NC_030597.1, I do find a standard stop codon after the extension (the first line below). We can check (at the protein level) if this...

Perhaps in the future, we can add an option to ask MitoZ not to do such a greedy extension if the users don't want, to make the annotation result more...