So I have tree file and metadata. Metadata includes sequence type ST (clusters that correspond in most part to the phylogeny), but also some patient data, age, sex etc.
I am trying to identify which ST has the highest percent of males etc. Would like to use information in phylo to strengthen analysis. And/or simply look at for clustering of e.g. high percent males in phylogeny irrespectively of ST.
Current idea is to find something in phytools (R) or similar, but would appreciate if the community here have any other suggestions. Phylogenetic independent contrasts?
Thanks in advance