I am a newbie to bioinformatics. I am trying to build phylogenetic trees using sequence data from multiple countries. For example, assume I have SARS-CoV-2 sequences from the UK and Brazil, with the difference being that the Gamma variants are sampled mostly from Brazil and Alpha variants from the UK, respectively. In this case, how to inform the phylogenetic package that all the sequences in the alignment file are from either of two different geographical locations? If I do not provide that information, I think the algorithm gives out results considering evolution happening in the same geographical location, which is not the case.
I am currently using BEAST and IQ-TREE. Thanks in advance for any help or leads.