threshStateC(x, thresholds)candidate_tree(x, method = c("unrooted", "ultrametric", "tipdated"),
eps = 1e-08, tip.dates = NULL, ...)
hash_phylo(x, ...)
coords(obj, dim = "3D")
map_duplicates(x, dist = length(x) < 500, ...)
pmlPen(object, lambda, ...)