Add reference genomes as an outgroup to a phylogenetic tree

Question

[Álvaro]

Hello,

I've build a Neighbour-Joining tree using a VCF file containing ~40 samples aligned to a reference genome. I used plink and a custom R script. Now I want to add the reference genomes of different species as an outgroup for the tree. How can I do it? Do I need to align those genomes to the one of the species that i'm working with? If so, how?

Thank you in advance :)