phy_tree(x) <- value

## S4 replacement method for signature 'phyloseq,phylo'
phy_tree(x) <- value

## S4 replacement method for signature 'phyloseq,phyloseq'
phy_tree(x) <- value

#
data("esophagus")
# An example of pruning to just the first 20 taxa in esophagus
ex2a <- prune_taxa(taxa_names(esophagus)[1:20], esophagus)
# The following 3 lines produces an ex2b that is equal to ex2a
ex2b <- ex2a
phy_tree(ex2b) <- phy_tree(esophagus)
identical(ex2a, ex2b)