Guanliang MENG

Hi [SongCU](https://github.com/SongCU), Thank you very much for the suggestion! I would test it and see if it works for most cases (because sometimes Perl=5.2.6 worked for me, but sometimes not,...

> hi @linzhi2013 . I have struggled fighting errors from cpamn during visualizing step. > > However when I installed MITOZ3 with `yml.file` above, it worked without any error messages!...

Hi Prunoideae, Sorry for my late reply, I have been busy recently. It's true that the dataset used has effect on results when using MitoZ. To my knowledge, different sizes...

To annotate these missing tRNAs, we will just have to use a more comprehensive tRNA database. MitoZ uses MiTFi to annotate tRNAs, and MiTFi provides their own HMM profiles along...

Hi, there is a message `All sequences are low abundance (

Hi Charles, Thanks for your suggestion! >I wonder if, as a feature request, it might be possible to change the error handling in these circumstances? A TypeError from Python isn't...

Hi Yang, thanks for the suggestion! I will think about it when I have more time. The Circos (http://circos.ca/) software is to make circular plots. You can also try to...

Maybe you can check this part: https://github.com/linzhi2013/MitoZ/wiki/Tutorial#6-broken-genes And this https://github.com/linzhi2013/MitoZ/wiki/The-%27mitoz-tools-gbfiletool%27-command `mitoz-tools gbfiletool` is only avaialable in the MitoZ 3.5-beta versions (https://github.com/linzhi2013/MitoZ/releases/tag/3.5-beta-1).

Hi James, `the overlap_information file is empty` means the assembled mitogenome is not complete, and thus there is no overlapping region at the beginning and end of the sequence. You...

Hi Abhijit, thanks for your question! MitoZ is designed for animal mitogenomes. Have you tried https://dogma.ccbb.utexas.edu/ ?