diff --git a/NAMESPACE b/NAMESPACE
index 6e305f41f..f02408886 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -99,6 +99,7 @@ export(unsplitOn)
 exportMethods("relabundance<-")
 exportMethods(ZTransform)
 exportMethods(addContaminantQC)
+exportMethods(addHierarchyTree)
 exportMethods(addNotContaminantQC)
 exportMethods(addPerSampleDominantFeatures)
 exportMethods(addPerSampleDominantTaxa)
@@ -130,6 +131,7 @@ exportMethods(getBestDMNFit)
 exportMethods(getDMN)
 exportMethods(getExperimentCrossAssociation)
 exportMethods(getExperimentCrossCorrelation)
+exportMethods(getHierarchyTree)
 exportMethods(getPrevalence)
 exportMethods(getPrevalentAbundance)
 exportMethods(getPrevalentFeatures)
diff --git a/NEWS b/NEWS
index 5972ab843..4bae25012 100644
--- a/NEWS
+++ b/NEWS
@@ -97,6 +97,7 @@ Changes in version 1.9.x
 Changes in version 1.11.x
 + loadFromMetaphlan: support strain rank
 + agglomerateByRank: agglomerate tree fix
++ Replace taxonomyTree and addTaxonomyTree with getHierarchyTree and addHierarchyTree
 + splitOn: update rowTree fix
 + perSampleDominantFeatures: add new arguments (n, other.name, complete)
 + loadFromMetaphlan: support "taxonomy" column for specifying taxonomy
diff --git a/R/deprecate.R b/R/deprecate.R
new file mode 100644
index 000000000..c2cbce75c
--- /dev/null
+++ b/R/deprecate.R
@@ -0,0 +1,40 @@
+#' These functions will be deprecated. Please use other functions instead.
+#' 
+#' @param x a \code{\link{SummarizedExperiment}} object -
+#' 
+#' @param ... -
+#' 
+#' @name deprecate
+NULL
+
+#' @rdname deprecate
+setGeneric("addTaxonomyTree",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("addTaxonomyTree"))
+
+#' @rdname deprecate
+#' @export
+setMethod("addTaxonomyTree", signature = c(x = "SummarizedExperiment"),
+            function(x){
+                .Deprecated(msg = paste0("'addTaxonomyTree' is deprecated.",
+                                        "Use 'addHierarchyTree' instead."))
+                addHierarchyTree(x)
+            }
+)
+
+#' @rdname deprecate
+setGeneric("taxonomyTree",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("taxonomyTree"))
+
+#' @rdname deprecate
+#' @export
+setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
+            function(x){
+                .Deprecated(msg = paste0("'taxonomyTree' is deprecated.",
+                                        "Use 'getHierarchyTree' instead."))
+                getHierarchyTree(x)
+            }
+)
diff --git a/R/splitOn.R b/R/splitOn.R
index b0dfc1198..7464d0bdb 100644
--- a/R/splitOn.R
+++ b/R/splitOn.R
@@ -97,9 +97,9 @@ NULL
 #' @rdname splitOn
 #' @export
 setGeneric("splitOn",
-           signature = "x",
-           function(x, ...)
-               standardGeneric("splitOn"))
+            signature = "x",
+            function(x, ...)
+                standardGeneric("splitOn"))
 
 # This function collects f (grouping variable), MARGIN, and 
 # use_names and returns them as a list.
@@ -108,8 +108,8 @@ setGeneric("splitOn",
     # Check f
     if(is.null(f)){
         stop("'f' must either be a single non-empty character value or",
-             " vector coercible to factor alongside the one of the dimensions of 'x'",
-             call. = FALSE)
+            " vector coercible to factor alongside the one of the dimensions of 'x'",
+            call. = FALSE)
     }
     # Check MARGIN
     if( !(is.null(MARGIN) || (is.numeric(MARGIN) && (MARGIN == 1 || MARGIN == 2 ))) ){
@@ -122,18 +122,18 @@ setGeneric("splitOn",
         # Check if the length of f matches with one of the dimensions
         if(!length(f) %in% dim(x)){
             stop("'f' must either be a single non-empty character value or",
-                 " vector coercible to factor alongside the on of the ",
-                 "dimensions of 'x'.",
-                 call. = FALSE)
+                " vector coercible to factor alongside the on of the ",
+                "dimensions of 'x'.",
+                call. = FALSE)
         # If it matches with both dimensions, give error if MARGIN is not specified
         } else if( is.null(MARGIN) && all(length(f) == dim(x)) ){
             stop("The length of 'f' matches with nrow and ncol. ",
-                 "Please specify 'MARGIN'.", call. = FALSE)
+                "Please specify 'MARGIN'.", call. = FALSE)
         # If MARGIN is specified but it does not match with length of f
         } else if( !is.null(MARGIN) && (length(f) !=  dim(x)[[MARGIN]]) ){
             stop("'f' does not match with ", 
-                 ifelse(MARGIN==1, "nrow", "ncol"), ". Please check 'MARGIN'.",
-                 call. = FALSE)
+                ifelse(MARGIN==1, "nrow", "ncol"), ". Please check 'MARGIN'.",
+                call. = FALSE)
         # IF f matches with nrow
         } else if(length(f) == dim(x)[[1]] && is.null(MARGIN)  ){
             MARGIN <- 1L
@@ -147,20 +147,20 @@ setGeneric("splitOn",
         if( !is.null(MARGIN) ){
             # Search from rowData or colData based on MARGIN
             dim_name <- switch(MARGIN,
-                               "1" = "rowData",
-                               "2" = "colData")
+                                "1" = "rowData",
+                                "2" = "colData")
             # Specify right function
             dim_FUN <- switch(MARGIN,
-                              "1" = retrieveFeatureInfo,
-                              "2" = retrieveCellInfo)
+                                "1" = retrieveFeatureInfo,
+                                "2" = retrieveCellInfo)
             # Try to get information
             tmp <- try({dim_FUN(x, f, search = dim_name)},
-                       silent = TRUE)
+                        silent = TRUE)
             # Give error if it cannot be found
             if(is(tmp,"try-error")){
                 stop("'f' is not found. ",
-                     "Please check that 'f' specifies a column from ", dim_name, ".", 
-                     call. = FALSE)
+                    "Please check that 'f' specifies a column from ", dim_name, ".", 
+                    call. = FALSE)
             }
             # Get values
             f <- tmp$value
@@ -168,22 +168,22 @@ setGeneric("splitOn",
         } else{
             # Try to get information from rowData
             tmp_row <- try({retrieveFeatureInfo(x, f, search = "rowData")},
-                           silent = TRUE)
+                            silent = TRUE)
             # Try to get information from colData
             tmp_col <- try({retrieveCellInfo(x, f, search = "colData")}, 
-                           silent = TRUE)
+                            silent = TRUE)
             
             # If it was not found 
             if( is(tmp_row, "try-error") && is(tmp_col, "try-error") ){
                 stop("'f' is not found. ",
-                     "Please check that 'f' specifies a column from ",
-                     "rowData or colData.", 
-                     call. = FALSE)
+                    "Please check that 'f' specifies a column from ",
+                    "rowData or colData.", 
+                    call. = FALSE)
                 # If f was found from both
             } else if( !is(tmp_row, "try-error") && !is(tmp_col, "try-error") ){
                 stop("'f' can be found from both rowData and colData. ",
-                     "Please specify 'MARGIN'.",
-                     call. = FALSE)
+                    "Please specify 'MARGIN'.",
+                    call. = FALSE)
                 # If it was found from rowData
             } else if( !is(tmp_row, "try-error") ){
                 MARGIN <- 1L
@@ -207,12 +207,12 @@ setGeneric("splitOn",
     # Check use_names
     if( !.is_a_bool(use_names) ){
         stop("'use_names' must be TRUE or FALSE.",
-             call. = FALSE)
+            call. = FALSE)
     }
     # Create a list from arguments
     list(f = f,
-         MARGIN = MARGIN,
-         use_names = use_names)
+        MARGIN = MARGIN,
+        use_names = use_names)
 }
 
 # PErform the split
@@ -221,8 +221,8 @@ setGeneric("splitOn",
     f <- args[["f"]]
     # Choose nrow or ncol based on MARGIN
     dim_FUN <- switch(args[["MARGIN"]],
-                      "1" = nrow,
-                      "2" = ncol)
+                        "1" = nrow,
+                        "2" = ncol)
     # Get indices from 1 to nrow/ncol
     idx <- seq_len(dim_FUN(x))
     # Split indices into groups based on grouping variable
@@ -276,12 +276,12 @@ setMethod("splitOn", signature = c(x = "SingleCellExperiment"),
 #' @export
 setMethod("splitOn", signature = c(x = "TreeSummarizedExperiment"),
     function(x, f = NULL, update_rowTree = FALSE,
-             ...){
+            ...){
         # Input check
         # Check update_rowTree
         if( !.is_a_bool(update_rowTree) ){
             stop("'update_rowTree' must be TRUE or FALSE.",
-                 call. = FALSE)
+                call. = FALSE)
         }
         # Input check end
         # Split data
@@ -289,7 +289,7 @@ setMethod("splitOn", signature = c(x = "TreeSummarizedExperiment"),
         # Manipulate rowTree or not?
         if( update_rowTree ){
             # If the returned value is a list, go through all of them
-            if( class(x) == "SimpleList" ){
+            if( is(x, 'SimpleList') ){
                 x <- SimpleList(lapply(x, .agglomerate_trees))
             } else {
                 # Otherwise, the returned value is TreeSE
@@ -306,9 +306,9 @@ setMethod("splitOn", signature = c(x = "TreeSummarizedExperiment"),
 #' @rdname splitOn
 #' @export
 setGeneric("unsplitOn",
-           signature = c("x"),
-           function(x, ...)
-               standardGeneric("unsplitOn"))
+            signature = c("x"),
+            function(x, ...)
+                standardGeneric("unsplitOn"))
 
 # Perform the unsplit
 .list_unsplit_on <- function(ses, update_rowTree = FALSE, MARGIN = NULL, ...){
@@ -316,13 +316,13 @@ setGeneric("unsplitOn",
     is_check <- vapply(ses,is,logical(1L),"SummarizedExperiment")
     if(!all(is_check)){
         stop("Input must be a list of SummarizedExperiment or derived objects ",
-             "only.",
-             call. = FALSE)
+            "only.",
+            call. = FALSE)
     }
     # Check update_rowTree
     if( !.is_a_bool(update_rowTree) ){
         stop("'update_rowTree' must be TRUE or FALSE.",
-             call. = FALSE)
+            call. = FALSE)
     }
     if( !(is.null(MARGIN) || (is.numeric(MARGIN) && (MARGIN == 1 || MARGIN == 2 ))) ){
         stop("'MARGIN' must be NULL, 1, or 2.", call. = FALSE )
@@ -339,15 +339,15 @@ setGeneric("unsplitOn",
     if( is.null(MARGIN) ){
         if( length(unique(dims[1L,])) == 1 && length(unique(dims[2L,])) == 1 ){
             stop("The dimensions match with row and column-wise. ",
-                 "Please specify 'MARGIN'.", call. = FALSE)
+                "Please specify 'MARGIN'.", call. = FALSE)
         } else if(length(unique(dims[1L,])) == 1L){
             MARGIN <- 2L
         } else if(length(unique(dims[2L,])) == 1L) {
             MARGIN <- 1L
         } else {
             stop("The dimensions are not equal across all elements. ", 
-                 "Please check that either number of rows or columns match.", 
-                 call. = FALSE)
+                "Please check that either number of rows or columns match.", 
+                call. = FALSE)
         }
     } else{
         # Get correct dimension, it is opposite of MARGIN
@@ -386,7 +386,7 @@ setGeneric("unsplitOn",
     if( class_x == "TreeSummarizedExperiment" ){
         # Update or add old tree from the first element of list
         if( update_rowTree ){
-            ans <- addTaxonomyTree(ans)
+            ans <- addHierarchyTree(ans)
         } else{
             rowTree(ans) <- rowTree(ses[[1L]])
         }
diff --git a/R/taxonomy.R b/R/taxonomy.R
index 0f70f1e8f..cc8d473c1 100644
--- a/R/taxonomy.R
+++ b/R/taxonomy.R
@@ -18,12 +18,6 @@
 #'   the lowest taxonomic information possible. If data from different levels,
 #'   is to be mixed, the taxonomic level is prepended by default.
 #'
-#' \code{taxonomyTree} generates a \code{phylo} tree object from the available
-#'   taxonomic information. Internally it uses
-#'   \code{\link[TreeSummarizedExperiment:toTree]{toTree}} and
-#'   \code{\link[TreeSummarizedExperiment:resolveLoop]{resolveLoop}} to sanitize
-#'   data if needed.
-#'
 #' \code{IdTaxaToDataFrame} extracts taxonomic results from results of
 #'   \code{\link[DECIPHER:IdTaxa]{IdTaxa}}.
 #'
@@ -40,11 +34,11 @@
 #'   object
 #'
 #' @param rank a single character defining a taxonomic rank. Must be a value of
-#'   \code{taxonomyRanks()} function.
+#'   \code{taxonomyRanks()} function
 #'
 #' @param empty.fields a \code{character} value defining, which values should be
 #'   regarded as empty. (Default: \code{c(NA, "", " ", "\t")}). They will be
-#'   removed if \code{na.rm = TRUE} before agglomeration.
+#'   removed if \code{na.rm = TRUE} before agglomeration
 #'
 #' @param with_rank \code{TRUE} or \code{FALSE}: Should the level be add as a
 #'   suffix? For example: "Phylum:Crenarchaeota" (default:
@@ -122,12 +116,6 @@
 #' mapTaxonomy(GlobalPatterns, taxa = "Escherichia")
 #' # returns information on a single output
 #' mapTaxonomy(GlobalPatterns, taxa = "Escherichia",to="Family")
-#'
-#' # adding a rowTree() based on the available taxonomic information. Please
-#' # note that any tree already stored in rowTree() will be overwritten.
-#' x <- GlobalPatterns
-#' x <- addTaxonomyTree(x)
-#' x
 NULL
 
 #' @rdname taxonomy-methods
@@ -139,8 +127,8 @@ TAXONOMY_RANKS <- c("domain","kingdom","phylum","class","order","family",
 
 #' @rdname taxonomy-methods
 setGeneric("taxonomyRanks", signature = c("x"),
-           function(x)
-             standardGeneric("taxonomyRanks"))
+            function(x)
+            standardGeneric("taxonomyRanks"))
 
 #' @rdname taxonomy-methods
 #'
@@ -156,10 +144,10 @@ setMethod("taxonomyRanks", signature = c(x = "SummarizedExperiment"),
 
 #' @rdname taxonomy-methods
 setGeneric("taxonomyRankEmpty",
-           signature = "x",
-           function(x, rank = taxonomyRanks(x)[1L],
+            signature = "x",
+            function(x, rank = taxonomyRanks(x)[1L],
                     empty.fields = c(NA, "", " ", "\t", "-", "_"))
-             standardGeneric("taxonomyRankEmpty"))
+            standardGeneric("taxonomyRankEmpty"))
 
 #' @rdname taxonomy-methods
 #' @aliases taxonomyRankEmpty
@@ -169,18 +157,18 @@ setGeneric("taxonomyRankEmpty",
 #' @export
 setMethod("taxonomyRankEmpty", signature = c(x = "SummarizedExperiment"),
     function(x, rank = taxonomyRanks(x)[1],
-           empty.fields = c(NA, "", " ", "\t", "-", "_")){
+            empty.fields = c(NA, "", " ", "\t", "-", "_")){
     # input check
     if(ncol(rowData(x)) == 0L){
         stop("rowData needs to be populated.", call. = FALSE)
     }
     if(!.is_non_empty_string(rank)){
         stop("'rank' must be an non empty single character value.",
-             call. = FALSE)
+            call. = FALSE)
     }
     if(!is.character(empty.fields) || length(empty.fields) == 0L){
         stop("'empty.fields' must be a character vector with one or ",
-             "more value", call. = FALSE)
+            "more value", call. = FALSE)
     }
     .check_taxonomic_rank(rank, x)
     .check_for_taxonomic_data_order(x)
@@ -191,9 +179,9 @@ setMethod("taxonomyRankEmpty", signature = c(x = "SummarizedExperiment"),
 
 #' @rdname taxonomy-methods
 setGeneric("checkTaxonomy",
-           signature = "x",
-           function(x, ...)
-             standardGeneric("checkTaxonomy"))
+            signature = "x",
+            function(x, ...)
+              standardGeneric("checkTaxonomy"))
 
 #' @rdname taxonomy-methods
 #' @aliases checkTaxonomy
@@ -232,8 +220,8 @@ setMethod("checkTaxonomy", signature = c(x = "SummarizedExperiment"),
     f <- tolower(ranks) %in% TAXONOMY_RANKS
     if(!any(f)){
         stop("no taxonomic ranks detected in rowData(). Columns with one of ",
-             "the following names can be used: '",
-             paste(TAXONOMY_RANKS, collapse = "', '"), "'", call. = FALSE)
+            "the following names can be used: '",
+            paste(TAXONOMY_RANKS, collapse = "', '"), "'", call. = FALSE)
     }
     m <- match(TAXONOMY_RANKS, tolower(ranks[f]))
     m <- m[!is.na(m)]
@@ -242,25 +230,25 @@ setMethod("checkTaxonomy", signature = c(x = "SummarizedExperiment"),
     check <- unique(c(m[-1], m[length(m)]) - m )
     if(!all(check %in% c(1L,0L))){
         stop("Taxonomic ranks are not in order. Please reorder columns, which ",
-             "correspond to taxonomic ranks like this:\n'",
-             paste(TAXONOMY_RANKS, collapse = "', '"), "'.",
-             call. = FALSE)
+            "correspond to taxonomic ranks like this:\n'",
+            paste(TAXONOMY_RANKS, collapse = "', '"), "'.",
+            call. = FALSE)
     }
 }
 
 
 #' @rdname taxonomy-methods
 setGeneric("getTaxonomyLabels",
-           signature = "x",
-           function(x, ...)
-               standardGeneric("getTaxonomyLabels"))
+            signature = "x",
+            function(x, ...)
+                standardGeneric("getTaxonomyLabels"))
 
 #' @rdname taxonomy-methods
 #' @aliases checkTaxonomy
 #' @export
 setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
     function(x, empty.fields = c(NA, "", " ", "\t", "-", "_"),
-             with_rank = FALSE, make_unique = TRUE, resolve_loops = FALSE, ...){
+            with_rank = FALSE, make_unique = TRUE, resolve_loops = FALSE, ...){
         # input check
         if(nrow(x) == 0L){
             stop("No data available in `x` ('x' has nrow(x) == 0L.)",
@@ -324,9 +312,9 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
             return(NULL)
         }
         stop("Only empty taxonomic information detected. Some rows contain ",
-             "only entries selected by 'empty.fields'. Cannot generated ",
-             "labels. Try option na.rm = TRUE in the function call.",
-             call. = FALSE)
+            "only entries selected by 'empty.fields'. Cannot generated ",
+            "labels. Try option na.rm = TRUE in the function call.",
+            call. = FALSE)
     }
     #
     if(is.matrix(tax_ranks_selected)){
@@ -352,9 +340,9 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
 }
 
 .get_taxonomic_label <- function(x,
-                                 empty.fields = c(NA, "", " ", "\t", "-", "_"),
-                                 with_rank = FALSE,
-                                 resolve_loops = FALSE){
+                                empty.fields = c(NA, "", " ", "\t", "-", "_"),
+                                with_rank = FALSE,
+                                resolve_loops = FALSE){
     rd <- rowData(x)
     tax_cols <- .get_tax_cols_from_se(x)
     tax_ranks_selected <- .get_tax_ranks_selected(x, rd, tax_cols, empty.fields)
@@ -372,9 +360,9 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
     #
     all_same_rank <- length(unique(tax_cols_selected)) == 1L
     ans <- mapply("[",
-                  as.data.frame(t(as.data.frame(rd))),
-                  tax_cols_selected,
-                  SIMPLIFY = FALSE)
+                    as.data.frame(t(as.data.frame(rd))),
+                    tax_cols_selected,
+                    SIMPLIFY = FALSE)
     ans <- unlist(ans, use.names = FALSE)
     if(with_rank || !all_same_rank){
         ans <- .add_taxonomic_type(rd, ans, tax_cols_selected)
@@ -382,21 +370,64 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
     ans
 }
 
-#' @rdname taxonomy-methods
-setGeneric("taxonomyTree",
-           signature = "x",
-           function(x, ...)
-               standardGeneric("taxonomyTree"))
+#' Calculate hierarchy tree
+#' 
+#' These functions generate a hierarchy tree using taxonomic information from a
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{SummarizedExperiment}}
+#' object and add this hierarchy tree into the \code{rowTree}.
+#' 
+#' \code{addHierarchyTree} calculates hierarchy tree from the available taxonomic
+#'   information and add it to \code{rowTree}.
+#'   
+#' \code{getHierarchyTree} generates a hierarchy tree from the available
+#'   taxonomic information. Internally it uses
+#'   \code{\link[TreeSummarizedExperiment:toTree]{toTree}} and
+#'   \code{\link[TreeSummarizedExperiment:resolveLoop]{resolveLoop}} to sanitize
+#'   data if needed.
+#' 
+#' @inheritParams taxonomy-methods
+#' 
+#' @return
+#' \itemize{
+#'   \item{\code{addHierarchyTree}:} {a \code{TreeSummarizedExperiment} whose
+#'   \code{phylo} tree represents the hierarchy among available taxonomy 
+#'   information}
+#'   \item{\code{getHierarchyTree}:} {a \code{phylo} tree representing the 
+#'   hierarchy among available taxonomy information.}
+#' }
+#' 
+#' @name hierarchy-tree
+#' 
+#' @examples
+#' # Generating a hierarchy tree based on available taxonomic information.
+#' data(GlobalPatterns)
+#' tse <- GlobalPatterns
+#' getHierarchyTree(tse)
+#' 
+#' # Adding a hierarchy tree based on the available taxonomic information. 
+#' # Please note that any tree already stored in rowTree() will be overwritten.
+#' tse <- addHierarchyTree(tse)
+#' tse
+#' 
+NULL
 
-#' @rdname taxonomy-methods
+#' @rdname hierarchy-tree
+setGeneric("getHierarchyTree",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("getHierarchyTree"))
+
+#' @rdname hierarchy-tree
+#' @aliases getHierarchyTree
 #' @export
-setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
+#' @importFrom ape drop.tip
+setMethod("getHierarchyTree", signature = c(x = "SummarizedExperiment"),
     function(x){
         # Input check
         # If there is no rowData it is not possible to create rowTree
         if( ncol(rowData(x)) == 0L ){
             stop("'x' does not have rowData. Tree cannot be created.", 
-                 call. = FALSE)
+                call. = FALSE)
         }
         #
         # Converted to data.frame so that drop = FALSE is enabled
@@ -414,32 +445,33 @@ setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
         for(i in rev(seq_len(ncol(td)))){
             if(any(td_NA[,i])){
                 to_drop <- paste0(colnames(td)[i],":",td[,i][td_NA[,i]])
-                tree <- ape::drop.tip(tree,
-                                      to_drop,
-                                      trim.internal = FALSE,
-                                      collapse.singles = FALSE)
+                tree <- drop.tip(
+                    tree,
+                    to_drop,
+                    trim.internal = FALSE,
+                    collapse.singles = FALSE)
             }
         }
         tree
     }
 )
 
-#' @rdname taxonomy-methods
-setGeneric("addTaxonomyTree",
-           signature = "x",
-           function(x, ...)
-               standardGeneric("addTaxonomyTree"))
+#' @rdname hierarchy-tree
+setGeneric("addHierarchyTree",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("addHierarchyTree"))
 
-#' @rdname taxonomy-methods
+#' @rdname hierarchy-tree
 #' @export
-setMethod("addTaxonomyTree", signature = c(x = "SummarizedExperiment"),
+setMethod("addHierarchyTree", signature = c(x = "SummarizedExperiment"),
     function(x){
         #
-        tree <- taxonomyTree(x)
+        tree <- getHierarchyTree(x)
         x <- as(x,"TreeSummarizedExperiment")
         rownames(x) <- getTaxonomyLabels(x, with_rank = TRUE,
-                                         resolve_loops = TRUE,
-                                         make_unique = FALSE)
+                                        resolve_loops = TRUE,
+                                        make_unique = FALSE)
         x <- changeTree(x, tree, rownames(x))
         x
     }
@@ -447,9 +479,9 @@ setMethod("addTaxonomyTree", signature = c(x = "SummarizedExperiment"),
 
 #' @rdname taxonomy-methods
 setGeneric("mapTaxonomy",
-           signature = "x",
-           function(x, ...)
-               standardGeneric("mapTaxonomy"))
+            signature = "x",
+            function(x, ...)
+                standardGeneric("mapTaxonomy"))
 
 #' @importFrom BiocGenerics %in% grepl
 .get_taxa_row_match <- function(taxa, td, from, use_grepl = FALSE){
@@ -490,33 +522,33 @@ setMethod("mapTaxonomy", signature = c(x = "SummarizedExperiment"),
         # input check
         if(!checkTaxonomy(x)){
             stop("Non compatible taxonomic information found. ",
-                 "checkTaxonomy(x) must be TRUE.",
-                 call. = FALSE)
+                "checkTaxonomy(x) must be TRUE.",
+                call. = FALSE)
         }
         if(!is.null(taxa)){
             if(!is.character(taxa)){
                 stop("'taxa' must be a character vector.",
-                     call. = FALSE)
+                    call. = FALSE)
             }
         }
         if(!is.null(from)){
             if(!.is_a_string(from)){
                 stop("'from' must be a single character value.",
-                     call. = FALSE)
+                    call. = FALSE)
             }
             if(!(from %in% taxonomyRanks(x))){
                 stop("'from' must be an element of taxonomyRanks(x).",
-                     call. = FALSE)
+                    call. = FALSE)
             }
         } 
         if(!is.null(to)){
             if(!.is_a_string(to)){
                 stop("'to' must be a single character value.",
-                     call. = FALSE)
+                    call. = FALSE)
             }
             if(!(to %in% taxonomyRanks(x))){
                 stop("'to' must be an element of taxonomyRanks(x).",
-                     call. = FALSE)
+                    call. = FALSE)
             }
         }
         if(!is.null(from) && !is.null(to)){
@@ -537,11 +569,11 @@ setMethod("mapTaxonomy", signature = c(x = "SummarizedExperiment"),
         c_f <- rep(TRUE,ncol(td))
         if(!is.null(from)){
             r_fs <- lapply(taxa, .get_taxa_row_match, td = td, from = from,
-                           use_grepl = use_grepl)
+                            use_grepl = use_grepl)
             names(r_fs) <- taxa
         } else {
             r_fs <- lapply(taxa, .get_taxa_any_match, td = td,
-                           use_grepl = use_grepl)
+                            use_grepl = use_grepl)
             names(r_fs) <- taxa
         }
         if(!is.null(to)) {
diff --git a/man/deprecate.Rd b/man/deprecate.Rd
new file mode 100644
index 000000000..56ec43586
--- /dev/null
+++ b/man/deprecate.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/deprecate.R
+\name{deprecate}
+\alias{deprecate}
+\alias{addTaxonomyTree}
+\alias{addTaxonomyTree,SummarizedExperiment-method}
+\alias{taxonomyTree}
+\alias{taxonomyTree,SummarizedExperiment-method}
+\title{These functions will be deprecated. Please use other functions instead.}
+\usage{
+addTaxonomyTree(x, ...)
+
+\S4method{addTaxonomyTree}{SummarizedExperiment}(x)
+
+taxonomyTree(x, ...)
+
+\S4method{taxonomyTree}{SummarizedExperiment}(x)
+}
+\arguments{
+\item{x}{a \code{\link{SummarizedExperiment}} object -}
+
+\item{...}{\itemize{
+\item 
+}}
+}
+\description{
+These functions will be deprecated. Please use other functions instead.
+}
diff --git a/man/hierarchy-tree.Rd b/man/hierarchy-tree.Rd
new file mode 100644
index 000000000..3f46234a2
--- /dev/null
+++ b/man/hierarchy-tree.Rd
@@ -0,0 +1,61 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/taxonomy.R
+\name{hierarchy-tree}
+\alias{hierarchy-tree}
+\alias{getHierarchyTree}
+\alias{getHierarchyTree,SummarizedExperiment-method}
+\alias{addHierarchyTree}
+\alias{addHierarchyTree,SummarizedExperiment-method}
+\title{Calculate hierarchy tree}
+\usage{
+getHierarchyTree(x, ...)
+
+\S4method{getHierarchyTree}{SummarizedExperiment}(x)
+
+addHierarchyTree(x, ...)
+
+\S4method{addHierarchyTree}{SummarizedExperiment}(x)
+}
+\arguments{
+\item{x}{a
+\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
+object}
+
+\item{...}{optional arguments not used currently.}
+}
+\value{
+\itemize{
+\item{\code{addHierarchyTree}:} {a \code{TreeSummarizedExperiment} whose
+\code{phylo} tree represents the hierarchy among available taxonomy
+information}
+\item{\code{getHierarchyTree}:} {a \code{phylo} tree representing the
+hierarchy among available taxonomy information.}
+}
+}
+\description{
+These functions generate a hierarchy tree using taxonomic information from a
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{SummarizedExperiment}}
+object and add this hierarchy tree into the \code{rowTree}.
+}
+\details{
+\code{addHierarchyTree} calculates hierarchy tree from the available taxonomic
+information and add it to \code{rowTree}.
+
+\code{getHierarchyTree} generates a hierarchy tree from the available
+taxonomic information. Internally it uses
+\code{\link[TreeSummarizedExperiment:toTree]{toTree}} and
+\code{\link[TreeSummarizedExperiment:resolveLoop]{resolveLoop}} to sanitize
+data if needed.
+}
+\examples{
+# Generating a hierarchy tree based on available taxonomic information.
+data(GlobalPatterns)
+tse <- GlobalPatterns
+getHierarchyTree(tse)
+
+# Adding a hierarchy tree based on the available taxonomic information. 
+# Please note that any tree already stored in rowTree() will be overwritten.
+tse <- addHierarchyTree(tse)
+tse
+
+}
diff --git a/man/taxonomy-methods.Rd b/man/taxonomy-methods.Rd
index 74d530b9f..d224bfa10 100644
--- a/man/taxonomy-methods.Rd
+++ b/man/taxonomy-methods.Rd
@@ -12,10 +12,6 @@
 \alias{checkTaxonomy,SummarizedExperiment-method}
 \alias{getTaxonomyLabels}
 \alias{getTaxonomyLabels,SummarizedExperiment-method}
-\alias{taxonomyTree}
-\alias{taxonomyTree,SummarizedExperiment-method}
-\alias{addTaxonomyTree}
-\alias{addTaxonomyTree,SummarizedExperiment-method}
 \alias{mapTaxonomy}
 \alias{mapTaxonomy,SummarizedExperiment-method}
 \alias{IdTaxaToDataFrame}
@@ -58,14 +54,6 @@ getTaxonomyLabels(x, ...)
   ...
 )
 
-taxonomyTree(x, ...)
-
-\S4method{taxonomyTree}{SummarizedExperiment}(x)
-
-addTaxonomyTree(x, ...)
-
-\S4method{addTaxonomyTree}{SummarizedExperiment}(x)
-
 mapTaxonomy(x, ...)
 
 \S4method{mapTaxonomy}{SummarizedExperiment}(x, taxa = NULL, from = NULL, to = NULL, use_grepl = FALSE)
@@ -78,11 +66,11 @@ IdTaxaToDataFrame(from)
 object}
 
 \item{rank}{a single character defining a taxonomic rank. Must be a value of
-\code{taxonomyRanks()} function.}
+\code{taxonomyRanks()} function}
 
 \item{empty.fields}{a \code{character} value defining, which values should be
 regarded as empty. (Default: \code{c(NA, "", " ", "\t")}). They will be
-removed if \code{na.rm = TRUE} before agglomeration.}
+removed if \code{na.rm = TRUE} before agglomeration}
 
 \item{...}{optional arguments not used currently.}
 
@@ -146,12 +134,6 @@ creation.
 the lowest taxonomic information possible. If data from different levels,
 is to be mixed, the taxonomic level is prepended by default.
 
-\code{taxonomyTree} generates a \code{phylo} tree object from the available
-taxonomic information. Internally it uses
-\code{\link[TreeSummarizedExperiment:toTree]{toTree}} and
-\code{\link[TreeSummarizedExperiment:resolveLoop]{resolveLoop}} to sanitize
-data if needed.
-
 \code{IdTaxaToDataFrame} extracts taxonomic results from results of
 \code{\link[DECIPHER:IdTaxa]{IdTaxa}}.
 
@@ -188,12 +170,6 @@ mapTaxonomy(GlobalPatterns)
 mapTaxonomy(GlobalPatterns, taxa = "Escherichia")
 # returns information on a single output
 mapTaxonomy(GlobalPatterns, taxa = "Escherichia",to="Family")
-
-# adding a rowTree() based on the available taxonomic information. Please
-# note that any tree already stored in rowTree() will be overwritten.
-x <- GlobalPatterns
-x <- addTaxonomyTree(x)
-x
 }
 \seealso{
 \code{\link[=agglomerate-methods]{agglomerateByRank}},
diff --git a/tests/testthat/test-2taxonomy.R b/tests/testthat/test-2taxonomy.R
index 9daaab994..ea06deab9 100644
--- a/tests/testthat/test-2taxonomy.R
+++ b/tests/testthat/test-2taxonomy.R
@@ -69,9 +69,9 @@ test_that("taxonomy", {
                  c("Family:j","Phylum:a","Family:k","Family:l","Family:m",
                    "Family:n","Family:o_1","Phylum:c","Family:o_2"))
 
-    # addTaxonomyTree
+    # addHierarchyTree
     data(GlobalPatterns, package="mia")
-    expect_warning(GlobalPatterns <- addTaxonomyTree(GlobalPatterns))
+    expect_warning(GlobalPatterns <- addHierarchyTree(GlobalPatterns))
     expect_equal(dim(GlobalPatterns),c(19216,26))
     expect_equal(rowTree(GlobalPatterns)$Nnode, 1089)
     expect_equal(length(rowTree(GlobalPatterns)$tip.label), 1645)