I am visualizing the alignment of a particular genomic region across different genomes with mauve. In certain genomes the region of interest is in the negative strand and in others the positive strand. What tool can I use to reverse complement my genbank files without losing the features and annotation?
I have not really used Mauve, so I don't know whether it might have an in-built setting for that.
SnapGene Viewer should be able to do that - it can open genbank files and export them, and View > Flip Sequence gets you the reverse complement without affecting the annotations. SnapGene can also do that; I only specified Viewer because it's free.
From the biology side of bioinformatics and the easier option, I would use Mauve. If you want to make the project more specific and tailored to your needs, and you have python skills, I would write Python code to complete this task. I would specifically use the bioinformatics Python library called Biopython: https://biopython.org pip install biopython
The second option is more involved but it gives you more control on your project/research since you're the one creating it. I personally would go with the 2nd option if you have coding skills. If you don't have coding skills, stick to the 1st option. Im sure there are also tools you can use that are found on Galaxy: https://usegalaxy.org
I am not sure what tools there are that would be good for your task and needs, but from using Galaxy in the past, im sure you can find something! :)