Masking Question

This is probably because of my incomplete understanding of the masking function, but I’ve made 2 trees, one under default values and one masking the 28880-28885 region to mask the N: 203 and N: 204 amino acids. I’ve included the nucleotide positions in the /defaults/parameters.yaml file. and nextalign, but the tree is identical for both runs and still displays the 203/204 regions. Is there a different file to input masking values in or has something changed in setting this up?

Hi @gvestal - the masked alignment is used to infer the tree topology and branch lengths, but the mutations shown on the tree (in auspice) are inferred from the unmasked alignment. Therefore you should still see mutations in the 28880-28885 region shown on both trees, but I would imagine the underlying tree is (slightly) different. As an example, we mask nuc21987 in our builds but still wish to show the different nucleotides across the tree rather than reporting that there are no changes in the sequencing data here.