I have been working on the mitochondrial genome but it is not my expert field.
I have extracted complete mitochondria from my whole genome sequenced samples. So far, I have used MEGA, DNASP and other related software. But I want to use Arlequin for population analysis but cannot figure out the proper pipeline. I have fasta format as well as fastq. Can anyone help me with the basics, please Also, I want to perform PCA and PCoA for different families in my dataset. I might know a few of these things but cannot figure out the ways and interpretations at the moment.
Your kind suggestions are way valuable.