Mitochondrial Annotator

What is it?

This tool annotates mitochondrial genomes based on a multiple alignment with already annotated closely related genomes. Essentially, it automates the steps you might do if you did such annotation manually. It loads gene coordinates form existing annotation, maps them on the multiple alignment, then uses this to obtain the coordinates of genes of the new genomes. This is all done under the assumption of the same gene set and gene order in all genomes, so it's only usable for closely related genomes.


We found that existing tools often produce wrong annotation on our genomes. We had to manually correct the coordinates of many genes. Therefore we decided to automate this relatively simple process, by using the available already annotated genomes as reference.


The script is available under the zlib/libpng license. The example data is in public domain.

Using it

Step 1. Prepare the multiple alignment of your genomes with reference genomes, stored in a FASTA file "alignment.fa".

Step 2. Collect the reference feature tables (corresponding to some of the genomes in the multiple alignment), and store them in a directory "input-tables".

Step 3. Run the annotator script "". If all goes well, you will find the new feature tables in a newly created directory "output-tables".


We share this script for the sake of transparency, because we are going to publish some of the data produced using this script. Although we found it useful for our data, we provide no guarantees whatsoever that it will work on your data. Careful inspection of the results are necessary in all cases.