What kind of software tool would you recommend as best suited to detect psbA-trnH inverisons? I am using R usually, however I cannot find any suitable packages. My sequences are in multiple .fasta files and I have around 30000 sequence in total.
These guys developed a pipeline: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498263/ However, thier web page is down.
I do want to identify the inversion and turn it around. I do not want to mask or delete it.