I'm struggling heavily with the following, and could use some in-depth help, perhaps over message or chat (I'd be happy to pay you for your time), with the following:
I have a dataset of whole genomes for 134 individuals of two species, one of the two species has two subspecies. I want to build a phylogeny incorporating my data, but need an outgroup. I want to use the Anna's Hummingbird genome off of ncbi, gather raw reads for an Anna's individual off ncbi, then align the raw reads to the genome. Since my current dataset was aligned to the Anna's genome, I want to combine this new Anna's individual bam file with my current dataset and produce the phylogeny. Please message me if you are interested in helping out. I've been on this for several days now. Thanks!