Hello,

I want to make a tree using BEAST with mitochondrial DNA sequences but I don't know how to partition the mitogenomes. I have a dataset of 118 mitogenomes from different genera that I aligned with MAFFT. I also have generated annotations for each of the unaligned sequences using MITOS2.

My question is, how can i tell any program (like PartitionFinder or BEAST) the positions of the genes or tRNAs when these positions differ between the samples. Also I don't know how to "transfer" the annotations from the raw sequences without gaps to the aligned sequences that do contain gaps. Is there any way to align against an annotated mitogenome?

Thank you in advance,

Álvaro