Combining multiple mtDNA loci in SuperCRUNCH

[Sam Fellows]

Hi,

I'm working with a dataset comprising GenBank sequences which I downloaded independent of SuperCRUNCH, sequences which I've scraped from supplemental materials that haven't made it onto GenBank, and a few other local sequences. The group consists of multiple samples per species for many genes. I'll be generating gene trees with my output (probably via a partitioned RAxML or IQ-Tree run) and then passing them along to ASTRAL-III for species tree building.

As I've assembled these data, I realized that my per species coverage would be much better if I treat the mtDNA genes (ND-1, ND-2, ND-4, 16S, and the occasional longer read including some of these) as a single concatenated gene rather than independent loci. This was a pretty straightforward issue when I was trying to extract genes from longer sequences, but does SuperCRUNCH have functionality to concatenate them again? Or should I just do this manually?

Finally, is there any reason that this would be a bad idea?

Thanks in advance!

Sam Fellows