diff --git a/NAMESPACE b/NAMESPACE
index d392d1279..6914af3d3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,10 @@ export(calculateOverlap)
 export(calculateRDA)
 export(calculateUnifrac)
 export(cluster)
+export(convertFromBIOM)
+export(convertFromDADA2)
+export(convertFromPhyloseq)
+export(convertToPhyloseq)
 export(countDominantFeatures)
 export(countDominantTaxa)
 export(estimateDivergence)
@@ -158,6 +162,7 @@ exportMethods(calculateOverlap)
 exportMethods(calculateUnifrac)
 exportMethods(checkTaxonomy)
 exportMethods(cluster)
+exportMethods(convertToPhyloseq)
 exportMethods(countDominantFeatures)
 exportMethods(countDominantTaxa)
 exportMethods(estimateDivergence)
diff --git a/NEWS b/NEWS
index 13f930df9..2fe5f540c 100644
--- a/NEWS
+++ b/NEWS
@@ -135,7 +135,10 @@ Changes in version 1.13.x
   includes the newly added subsampled assay.
 + Fix bug in mergeFeaturesByPrevalence
 + new aliases calculateDPCoA to getDPCoA, calculateNMDS to getNMDS, calculateRDA to getRDA, 
-calculateCCA to getCCA
+  calculateCCA to getCCA
++ add informative error message in rarefyAssay on assays with strictly-negative values 
 + add informative error message in rarefyAssay on assays with strictly-negative values 
 + Use rbiom package in unifrac implementation
 + Updated parameter names to follow naming convention "parameter.name"
++ rename makeTreeSEFrom* and makePhyloseqFromTreeSE functions and combine their
+  documentation under new manual page convert
diff --git a/R/makeTreeSummarizedExperimentFromBiom.R b/R/convertFromBIOM.R
similarity index 84%
rename from R/makeTreeSummarizedExperimentFromBiom.R
rename to R/convertFromBIOM.R
index 0f385ae33..7003c32bf 100644
--- a/R/makeTreeSummarizedExperimentFromBiom.R
+++ b/R/convertFromBIOM.R
@@ -1,10 +1,16 @@
-#' Loading a biom file
+#' Converters
 #'
-#' For convenience a few functions are available to convert data from a
-#' \sQuote{biom} file or object into a
+#' For convenience a few functions are available to convert BIOM, DADA2 and 
+#' phyloseq objects to 
 #' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#' objects and 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#' objects to phyloseq objects.
 #'
-#' @param file biom file location
+#' @param file BIOM file location
+#' 
+#' @param obj BIOM object to be converted to a 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
 #' 
 #' @param prefix.rm \code{TRUE} or \code{FALSE}: Should
 #' taxonomic prefixes be removed? The prefixes is removed only from detected
@@ -27,22 +33,31 @@
 #' 
 #' @param ... additional arguments 
 #'   \itemize{
-#'        \item \code{patter}: \code{character} value specifying artifacts
+#'        \item{\code{pattern}}{\code{character} value specifying artifacts
 #'        to be removed. If \code{patterns = "auto"}, special characters
-#'        are removed. (default: \code{pattern = "auto"})
+#'        are removed. (default: \code{pattern = "auto"}) 
+#'        } 
 #'    }
 #' 
-#' @return An object of class
+#' @details 
+#' \code{convertFromBIOM} coerces a BIOM object to a 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#' object.
+#' 
+#' \code{importBIOM} loads a BIOM file and creates a 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}} 
+#' object from the BIOM object contained in the loaded file
+#' @return 
+#' \code{importBIOM} returns an object of class
+#'   \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#'   
+#' \code{convertFromBIOM} returns an object of class
 #'   \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
 #'
-#' @name makeTreeSEFromBiom
-#' @seealso
-#' \code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-#' \code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
-#' \code{\link[=importQIIME2]{importQIIME2}}
-#' \code{\link[=importMothur]{importMothur}}
+#' @name convert
 #'
 #' @examples
+#' ### Load and convert BIOM results to a TreeSE
 #' # Load biom file
 #' library(biomformat)
 #' biom_file <- system.file("extdata", "rich_dense_otu_table.biom",
@@ -53,7 +68,7 @@
 #' 
 #' # Make TreeSE from biom object
 #' biom_object <- biomformat::read_biom(biom_file)
-#' tse <- makeTreeSEFromBiom(biom_object)
+#' tse <- convertFromBIOM(biom_object)
 #' 
 #' # Get taxonomyRanks from prefixes and remove prefixes
 #' tse <- importBIOM(biom_file,
@@ -69,31 +84,30 @@
 #'                     artifact.rm = TRUE)
 NULL
 
-#' @rdname makeTreeSEFromBiom
-#'
+#' \code{importBIOM} loads a BIOM file and creates a TreeSE from the BIOM object
+#' contained in the loaded file.
+#' @rdname convert
 #' @export
 importBIOM <- function(file, ...) {
     .require_package("biomformat")
     biom <- biomformat::read_biom(file)
-    makeTreeSEFromBiom(biom, ...)
+    convertFromBIOM(biom,...)
 }
 
-#' @rdname makeTreeSEFromBiom
-#'
-#' @param x object of type \code{\link[biomformat:read_biom]{biom}}
-#'
-#' @export
+#' \code{convertFromBIOM} creates a TreeSE object from a BIOM object.
 #' @importFrom S4Vectors make_zero_col_DFrame DataFrame
 #' @importFrom dplyr %>% bind_rows
-makeTreeSEFromBiom <- function(
-        x, prefix.rm = removeTaxaPrefixes, 
+#' @rdname convert
+#' @export
+convertFromBIOM <- function(
+        obj, prefix.rm = removeTaxaPrefixes, 
         removeTaxaPrefixes = FALSE, rank.from.prefix = rankFromPrefix, 
         rankFromPrefix = FALSE,
         artifact.rm = remove.artifacts, remove.artifacts = FALSE, ...){
     # input check
     .require_package("biomformat")
-    if(!is(x,"biom")){
-        stop("'x' must be a 'biom' object", call. = FALSE)
+    if(!is(obj,"biom")){
+        stop("'obj' must be a 'biom' object", call. = FALSE)
     }
     if( !.is_a_bool(prefix.rm) ){
         stop("'prefix.rm' must be TRUE or FALSE.", call. = FALSE)
@@ -105,9 +119,9 @@ makeTreeSEFromBiom <- function(
         stop("'artifact.rm' must be TRUE or FALSE.", call. = FALSE)
     }
     #
-    counts <- as(biomformat::biom_data(x), "matrix")
-    sample_data <- biomformat::sample_metadata(x)
-    feature_data <- biomformat::observation_metadata(x)
+    counts <- as(biomformat::biom_data(obj), "matrix")
+    sample_data <- biomformat::sample_metadata(obj)
+    feature_data <- biomformat::observation_metadata(obj)
     
     # colData is initialized with empty tables with rownames if it is NULL
     if( is.null(sample_data) ){
@@ -185,8 +199,8 @@ makeTreeSEFromBiom <- function(
     }
     
     # Adjust row and colnames
-    rownames(counts) <- rownames(feature_data) <- biomformat::rownames(x)
-    colnames(counts) <- rownames(sample_data) <- biomformat::colnames(x)
+    rownames(counts) <- rownames(feature_data) <- biomformat::rownames(obj)
+    colnames(counts) <- rownames(sample_data) <- biomformat::colnames(obj)
     
     # Convert into DataFrame
     sample_data <- DataFrame(sample_data)
@@ -202,14 +216,6 @@ makeTreeSEFromBiom <- function(
     return(tse)
 }
 
-####################### makeTreeSummarizedExperimentFromBiom ###################
-#' @param x object of type \code{\link[biomformat:read_biom]{biom}}
-#' @rdname makeTreeSEFromBiom
-#' @export
-makeTreeSummarizedExperimentFromBiom <- function(x, ...){
-    makeTreeSEFromBiom(x, ...)
-}
-
 ################################ HELP FUNCTIONS ################################
 # This function removes prefixes from taxonomy names
 .remove_prefixes_from_taxa <- function(
diff --git a/R/makeTreeSummarizedExperimentFromDADA2.R b/R/convertFromDADA2.R
similarity index 53%
rename from R/makeTreeSummarizedExperimentFromDADA2.R
rename to R/convertFromDADA2.R
index c026c5d24..bd39333d1 100644
--- a/R/makeTreeSummarizedExperimentFromDADA2.R
+++ b/R/convertFromDADA2.R
@@ -1,44 +1,41 @@
 #' Coerce \sQuote{DADA2} results to \code{TreeSummarizedExperiment}
 #'
-#' \code{makeTreeSEFromDADA2} is a wrapper for the
-#' \code{mergePairs} function from the \code{dada2} package.
-#'
-#' @param ... See \code{mergePairs} function for
-#'   more details.
+#' @param ... Addional arguments. For \code{convertFromDADA2}, see 
+#' \code{mergePairs} function for more details.
 #'
 #' @details
-#' A count matrix is constructed via \code{makeSequenceTable(mergePairs(...))}
-#' and rownames are dynamically created as \code{ASV(N)} with \code{N} from
-#' 1 to \code{nrow} of the count tables. The colnames and rownames from the
-#' output of \code{makeSequenceTable} are stored as \code{colnames} and in the
-#' \code{referenceSeq} slot of the \code{TreeSummarizedExperiment},
-#' respectively.
+#' \code{convertFromDADA2} is a wrapper for the
+#' \code{mergePairs} function from the \code{dada2} package.
+#' A count matrix is constructed via 
+#' \code{makeSequenceTable(mergePairs(...))} and rownames are dynamically 
+#' created as \code{ASV(N)} with \code{N} from 1 to \code{nrow} of the count 
+#' tables. The colnames and rownames from the output of \code{makeSequenceTable}
+#' are stored as \code{colnames} and in the \code{referenceSeq} slot of the 
+#' \code{TreeSummarizedExperiment},respectively.
 #'
-#' @return An object of class \code{TreeSummarizedExperiment}
+#' @return \code{convertFromDADA2} returns an object of class 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
 #'
 #' @importFrom S4Vectors SimpleList
 #' @importFrom Biostrings DNAStringSet
 #'
-#' @name makeTreeSEFromDADA2
-#' @seealso
-#' \code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-#' \code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-#' \code{\link[=importQIIME2]{importQIIME2}}
-#' \code{\link[=importMothur]{importMothur}}
+#' @rdname convert
 #'
 #' @export
 #'
 #' @examples
+#' 
+#' ### Coerce DADA2 results to a TreeSE object
 #' if(requireNamespace("dada2")) {
 #'   fnF <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
 #'   fnR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
 #'   dadaF <- dada2::dada(fnF, selfConsist=TRUE)
 #'   dadaR <- dada2::dada(fnR, selfConsist=TRUE)
 #'
-#'   tse <- makeTreeSEFromDADA2(dadaF, fnF, dadaR, fnR)
+#'   tse <- convertFromDADA2(dadaF, fnF, dadaR, fnR)
 #'   tse
 #' }
-makeTreeSEFromDADA2 <- function(...) {
+convertFromDADA2 <- function(...) {
     # input checks
     .require_package("dada2")
     .require_package("stringr")
@@ -62,12 +59,3 @@ makeTreeSEFromDADA2 <- function(...) {
     rownames(output) <- rName
     output
 }
-
-#################### makeTreeSummarizedExperimentFromDADA2 #####################
-#' @param ... See \code{mergePairs} function for
-#'   more details.
-#' @name makeTreeSEFromDADA2
-#' @export
-makeTreeSummarizedExperimentFromDADA2 <- function(...) {
-    makeTreeSEFromDADA2(...)
-}
diff --git a/R/convertFromPhyloseq.R b/R/convertFromPhyloseq.R
new file mode 100644
index 000000000..1753798a5
--- /dev/null
+++ b/R/convertFromPhyloseq.R
@@ -0,0 +1,77 @@
+#' @param phy a \code{phyloseq} object
+#' 
+#' @details 
+#' \code{convertFromPhyloseq} converts \code{phyloseq}
+#' objects into 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}} objects.
+#' All data stored in a \code{phyloseq} object is transferred.
+#'
+#' @return 
+#' \code{convertFromPhyloseq} returns an object of class 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#'
+#' @importFrom S4Vectors SimpleList DataFrame make_zero_col_DFrame
+#' @importFrom SummarizedExperiment colData colData<-
+#'
+#' @export
+#'
+#' @rdname convert
+#' @seealso
+#' \code{\link[=importQIIME2]{importQIIME2}}
+#' \code{\link[=importMothur]{importMothur}}
+#'
+#' @examples
+#' 
+#' ### Coerce a phyloseq object to a TreeSE object
+#' if (requireNamespace("phyloseq")) {
+#'     data(GlobalPatterns, package="phyloseq")
+#'     convertFromPhyloseq(GlobalPatterns)
+#'     data(enterotype, package="phyloseq")
+#'     convertFromPhyloseq(enterotype)
+#'     data(esophagus, package="phyloseq")
+#'     convertFromPhyloseq(esophagus)
+#' }
+convertFromPhyloseq <- function(phy, ...) {
+    # input check
+    .require_package("phyloseq")
+    if(!is(phy,"phyloseq")){
+        stop("'phy' must be a 'phyloseq' object")
+    }
+    #
+    # Get the assay
+    counts <- phy@otu_table@.Data
+    # Check the orientation, and transpose if necessary
+    if( !phy@otu_table@taxa_are_rows ){
+        counts <- t(counts)
+    }
+    # Create a list of assays
+    assays <- SimpleList(counts = counts)
+    
+    if(!is.null(phy@tax_table@.Data)){
+        rowData <- DataFrame(data.frame(phy@tax_table@.Data))
+    } else{
+        rowData <- S4Vectors::make_zero_col_DFrame(nrow(assays$counts))
+        rownames(rowData) <- rownames(assays$counts)
+    }
+    if(!is.null(phy@sam_data)){
+        colData <- DataFrame(data.frame(phy@sam_data))
+    } else{
+        colData <- S4Vectors::make_zero_col_DFrame(ncol(assays$counts))
+        rownames(colData) <- colnames(assays$counts)
+    }
+    if(!is.null(phy@phy_tree)){
+        rowTree <- phy@phy_tree
+    } else {
+        rowTree <- NULL
+    }
+    if (!is.null(phy@refseq)) {
+        referenceSeq <- phy@refseq
+    } else {
+        referenceSeq <- NULL
+    }
+    TreeSummarizedExperiment(assays = assays,
+                            rowData = rowData,
+                            colData = colData,
+                            rowTree = rowTree,
+                            referenceSeq = referenceSeq)
+}
diff --git a/R/convertToPhyloseq.R b/R/convertToPhyloseq.R
new file mode 100644
index 000000000..1240140ff
--- /dev/null
+++ b/R/convertToPhyloseq.R
@@ -0,0 +1,264 @@
+#' Create a phyloseq object from a TreeSummarizedExperiment object
+#' 
+#' @param x a 
+#'   \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#'   object
+#'   
+#' @param assay.type A single character value for selecting the
+#'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}} to be
+#'   included in the phyloseq object that is created. 
+#'   (By default: \code{assay.type = "counts"})
+#'   
+#' @param assay_name a single \code{character} value for specifying which
+#'   assay to use for calculation.
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
+#'   will be disabled.)
+#'   
+#' @param tree.name a single \code{character} value for specifying which
+#'   tree will be included in the phyloseq object that is created, 
+#'   (By default: \code{tree.name = "phylo"})
+#'   
+#' @param tree_name a single \code{character} value for specifying which
+#'   tree will be included in the phyloseq object that is created, 
+#'   (By default: \code{tree_name = "phylo"})
+#'   \code{tree_name} will be deprecated. Use \code{tree.name} instead.
+#' 
+#' @details 
+#' \code{convertToPhyloseq} creates a phyloseq object from a 
+#' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+#' object. By using \code{assay.type}, it is possible to specify which table
+#' from \code{assay} is added to the phyloseq object.
+#'
+#' @return
+#' \code{convertToPhyloseq} returns an object of class 
+#' \code{\link[phyloseq:phyloseq-class]{phyloseq}}
+#'
+#' @author Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
+#'
+#' @examples
+#' 
+#' ### Coerce a TreeSE object to a phyloseq object
+#' # Get tse object
+#' data(GlobalPatterns)
+#' tse <- GlobalPatterns
+#'
+#' # Create a phyloseq object from it
+#' phy <- convertToPhyloseq(tse)
+#' phy
+#'
+#' # By default the chosen table is counts, but if there are other tables,
+#' # they can be chosen with assay.type.
+#'
+#' # Counts relative abundances table
+#' tse <- transformAssay(tse, method = "relabundance")
+#' phy2 <- convertToPhyloseq(tse, assay.type = "relabundance")
+#' phy2
+#' @rdname convert
+#' @export
+setGeneric("convertToPhyloseq", signature = c("x"),
+           function(x, ...)
+             standardGeneric("convertToPhyloseq"))
+
+#' @rdname convert
+#' @export
+setMethod("convertToPhyloseq",
+          signature = c(x = "SummarizedExperiment"),
+    function(x, assay.type = "counts", assay_name = NULL, ...){
+      # Input check
+      .require_package("phyloseq")
+      # Check that tse do not have zero rows
+      if(!all(dim(x) > 0)){
+        stop("'x' contains zero rows. 'x' can not be converted
+             to a phyloseq object.",
+             call. = FALSE)
+      }
+      
+      if (!is.null(assay_name)) {
+        .Deprecated(old="assay_name", new="assay.type", "Now assay_name is deprecated. Use assay.type instead.")
+      }
+      
+      # Check assay.type
+      .check_assay_present(assay.type, x)
+      
+      # phyloseq object requires nonduplicated rownames. If there are 
+      # duplicated rownames, they are converted so that they are unique
+      if( any(duplicated(rownames(x))) ){
+        rownames(x) <- getTaxonomyLabels(x)
+      }
+      # List of arguments
+      args = list()
+      # Gets the abundance data from assay, and converts it to otu_table
+      otu_table <- as.matrix(assay(x, assay.type))
+      otu_table <- phyloseq::otu_table(otu_table, taxa_are_rows = TRUE)
+      # Adds to the list
+      args[["otu_table"]] <- otu_table
+      
+      # If rowData includes information
+      if(!( length(rowData(x)[,taxonomyRanks(x)]) == 0 ||
+            is.null((rowData(x)[,taxonomyRanks(x)])) )){
+        # Converts taxonomy table to characters if it's not already
+        rowData(x) <- DataFrame(lapply(rowData(x), as.character))
+        # Gets the taxonomic data from rowData, and converts it to tax_table
+        tax_table <- as.matrix(rowData(x)[,taxonomyRanks(x),drop=FALSE])
+        tax_table <- phyloseq::tax_table(tax_table)
+        # Adds to the list
+        args[["tax_table"]] <- tax_table
+      }
+      
+      # If colData includes information
+      if(!( length(colData(x)) == 0 || is.null(ncol(colData(x))) )){
+        # Gets the feature_data from colData and converts it to sample_data
+        sample_data <- as.data.frame(colData(x))
+        sample_data <- phyloseq::sample_data(sample_data)
+        # Adds to the list
+        args[["sample_data"]] <- sample_data
+      }
+      
+      # Creates a phyloseq object
+      phyloseq <- do.call(phyloseq::phyloseq, args)
+      return(phyloseq)
+    }
+)
+
+#' @rdname convert
+#' @export
+setMethod("convertToPhyloseq",
+          signature = c(x = "TreeSummarizedExperiment"),
+    function(x, tree.name = tree_name, tree_name = "phylo", ...){
+      # If rowTrees exist, check tree.name
+      if( length(x@rowTree) > 0 ){
+        .check_rowTree_present(tree.name, x)
+        # Subset the data based on the tree
+        x <- x[ rowLinks(x)$whichTree == tree.name, ]
+        add_phy_tree <- TRUE
+      } else{
+        add_phy_tree <- FALSE
+      }
+      #
+      
+      # phyloseq and tree objects require nonduplicated rownames. If there are 
+      # duplicated rownames, they are converted so that they are unique
+      if( any(duplicated(rownames(x))) ){
+        rownames(x) <- getTaxonomyLabels(x)
+      }
+      # Gets otu_table object from the function above this, if tse contains
+      # only abundance table.
+      # Otherwise, gets a phyloseq object with otu_table, and tax_table
+      # and/or sample_data
+      obj <- callNextMethod()
+      # List of arguments
+      args = list()
+      # Adds to the list of arguments, if 'obj' is not a phyloseq object
+      # i.e. is an otu_table
+      if(!is(obj,"phyloseq")){
+        # Adds otu_table to the list
+        args[["otu_table"]] <- obj
+      }
+      
+      # Add phylogenetic tree
+      if( add_phy_tree ){
+        phy_tree <- .get_rowTree_for_phyloseq(x, tree.name)
+        # If the object is a phyloseq object, adds phy_tree to it
+        if(is(obj,"phyloseq")){
+          phyloseq::phy_tree(obj) <- phy_tree
+        } else{
+          # Adds to the list
+          args[["phy_tree"]] <- phy_tree
+        }
+      }
+      
+      # If referenceSeq has information, stores it to refseq and converts is
+      # to phyloseq's refseq.
+      if( !is.null(referenceSeq(x)) ){
+        # Get referenceSeqs
+        refseq <- .get_referenceSeq_for_phyloseq(x, ...)
+        # IF refSeq passed the test, add it
+        if( !is.null(refseq) ){
+          # Convert it to phyloseq object
+          refseq <- phyloseq::refseq(refseq)
+          # If the object is a phyloseq object, adds refseq to it
+          if(is(obj,"phyloseq")){
+            obj <- phyloseq::merge_phyloseq(obj, refseq)
+          } else{
+            # Adds to the list
+            args[["refseq"]] <- refseq
+          }
+        }
+      }
+      
+      # If 'obj' is not a phyloseq object, creates one.
+      if(!is(obj,"phyloseq")){
+        # Creates a phyloseq object
+        phyloseq <- do.call(phyloseq::phyloseq, args)
+      } else{
+        phyloseq <- obj
+      }
+      phyloseq
+    }
+)
+
+
+################################ HELP FUNCTIONS ################################
+# If tips do not match with rownames, prune the tree
+.get_x_with_pruned_tree <- function(x, tree.name){
+    # Get rowLinks
+    row_links <- rowLinks(x)
+    # Gets node labels
+    node_labs <- row_links[ , "nodeLab"]
+    # Prunes the tree
+    tree_pruned <- ape::keep.tip(rowTree(x), node_labs)
+    # Replace tip labels with corresponding rownames
+    tree_pruned$tip.label <- rownames(x)
+    # Assigns the pruned tree back to TSE object
+    rowTree(x) <- tree_pruned
+    warning("Tips of rowTree are renamed to match rownames.", call. = FALSE)
+    return(x)
+}
+
+# In phyloseq, tips and rownames must match
+.get_rowTree_for_phyloseq <- function(x, tree.name){
+    # Check if the rowTree's tips match with rownames:
+    # tips labels are found from rownames
+    if( any(!( rowTree(x, tree.name)$tip.label) %in% rownames(x)) ){
+        # If rowtree do not match, tree is pruned
+        x <- .get_x_with_pruned_tree(x, tree.name)
+    }
+    # Get rowTree
+    phy_tree <- rowTree(x, tree.name)
+    # Convert rowTree to phyloseq object
+    phy_tree <- phyloseq::phy_tree(phy_tree)
+        
+    return(phy_tree)
+}
+
+.get_referenceSeq_for_phyloseq <- function(x, referenceSeq = 1, ...){
+    # Get reference seqs
+    refSeqs <- referenceSeq(x)
+    # Is referenceSeq a list / does it contain multiple DNA sets
+    is_list <- is(refSeqs, "DNAStringSetList")
+    
+    # Take only one set, if it is a list
+    if( is_list ){
+        # Check referenceSeq
+        if( !( (.is_non_empty_string(referenceSeq) && referenceSeq %in% names(refSeqs)) ||
+            (.is_an_integer(referenceSeq) && (referenceSeq>0 && referenceSeq<=length(refSeqs))) )
+            ){
+            stop("'referenceSeq' must be a non-empty single character value or an integer ",
+                 "specifying the DNAStringSet from DNAStringSetList.",
+                 call. = FALSE)
+        }
+        # Get specified referenceSeq
+        refSeqs <- refSeqs[[referenceSeq]]
+        warning("Use 'referenceSeq' to specify DNA set from DNAStringSetList. ",
+                "Current choice is '", referenceSeq, "'.", 
+                call. = FALSE)
+    }
+    # Check if all rownames have referenceSeqs
+    if( !(all(rownames(x) %in% names(refSeqs)) &&
+        all(names(refSeqs) %in% rownames(x) )) ){
+        warning("referenceSeq does not match with rownames so they are discarded.",
+                call. = FALSE)
+        refSeqs <- NULL
+    }
+    return(refSeqs)
+}
diff --git a/R/deprecate.R b/R/deprecate.R
index 520620661..e1312dd30 100644
--- a/R/deprecate.R
+++ b/R/deprecate.R
@@ -1,8 +1,6 @@
 #' These functions will be deprecated. Please use other functions instead.
 #' 
-#' @param x A
-#'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
-#'   object.
+#' @param x an object
 #'    
 #' @param ... Additional parameters. See dedicated function.
 #' 
@@ -59,6 +57,23 @@ setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
             }
 )
 
+#' @rdname deprecate
+#' @export
+setGeneric("makeTreeSummarizedExperimentFromPhyloseq", signature = c("x"),
+            function(x)
+                standardGeneric("makeTreeSummarizedExperimentFromPhyloseq"))
+
+#' @rdname deprecate
+#' @export
+setMethod("makeTreeSummarizedExperimentFromPhyloseq", 
+            signature = c(x = "ANY"), function(x){
+                .Deprecated(msg = paste0(
+                    "'makeTreeSummarizedExperimentFromPhyloseq' is deprecated.",
+                    " Use 'convertFromPhyloseq' instead."))
+                convertFromPhyloseq(x)
+            }
+)
+
 #' @rdname deprecate
 #' @export
 setGeneric("mergeRows",
@@ -79,6 +94,40 @@ setMethod("mergeRows", signature = c(x = "SummarizedExperiment"),
 
 #' @rdname deprecate
 #' @export
+setGeneric("makePhyloseqFromTreeSummarizedExperiment", signature = c("x"),
+            function(x, ...)
+                standardGeneric("makePhyloseqFromTreeSummarizedExperiment"))
+
+#' @rdname deprecate
+#' @export
+setMethod("makePhyloseqFromTreeSummarizedExperiment", 
+            signature = c(x = "ANY"), function(x, ...){
+                .Deprecated(msg = paste0(
+                    "'makePhyloseqFromTreeSummarizedExperiment' is deprecated.",
+                    " Use 'convertToPhyloseq' instead."))
+                convertToPhyloseq(x, ...)
+            }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("makePhyloseqFromTreeSE", signature = c("x"),
+           function(x, ...)
+               standardGeneric("makePhyloseqFromTreeSE"))
+
+#' @rdname deprecate
+#' @export
+setMethod("makePhyloseqFromTreeSE", 
+          signature = c(x = "ANY"), function(x, ...){
+              .Deprecated(msg = paste0(
+                  "'makePhyloseqFromTreeSE' is deprecated.",
+                  " Use 'convertToPhyloseq' instead."))
+              convertToPhyloseq(x, ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export               
 setMethod("mergeRows", signature = c(x = "TreeSummarizedExperiment"),
           function(x, ...){
               .Deprecated(msg = paste0("'mergeRows' is deprecated. ",
@@ -222,6 +271,51 @@ setMethod("mergeFeaturesByPrevalence", signature = c(x = "SummarizedExperiment")
           }
 )
 
+#' @rdname deprecate
+#' @export
+makeTreeSEFromBiom <- function(...){
+    .Deprecated(msg = paste0(
+        "'makeTreeSEFromBiom' is deprecated.",
+        " Use 'convertFromBIOM' instead."))
+    convertFromBIOM(...)
+}
+
+#' @rdname deprecate
+#' @export
+makeTreeSummarizedExperimentFromBiom <- function(...){
+    .Deprecated(msg = paste0(
+        "'makeTreeSummarizedExperimentFromBiom' is deprecated.",
+        " Use 'convertFromBIOM' instead."))
+    convertFromBIOM(...)
+}
+
+#' @rdname deprecate
+#' @export
+makeTreeSEFromDADA2 <- function(...) {
+    .Deprecated(msg = paste0(
+        "'makeTreeSEFromDADA2' is deprecated.",
+        " Use 'convertFromDADA2' instead."))
+    convertFromDADA2(...)
+}
+
+#' @rdname deprecate
+#' @export
+makeTreeSummarizedExperimentFromDADA2 <- function(...) {
+    .Deprecated(msg = paste0(
+        "'makeTreeSummarizedExperimentFromDADA2' is deprecated.",
+        " Use 'convertFromDADA2' instead."))
+    convertFromDADA2(...)
+}
+
+#' @rdname deprecate
+#' @export
+makeTreeSEFromPhyloseq <- function(x) {
+    .Deprecated(msg = paste0(
+        "'makeTreeSEFromPhyloseq' is deprecated.",
+        " Use 'convertFromPhyloseq' instead."))
+    convertFromPhyloseq(...)
+}
+
 #' @rdname deprecate
 #' @export
 setGeneric("getExperimentCrossAssociation", signature = c("x"),
diff --git a/R/importHumann.R b/R/importHumann.R
index a35e2c1a1..3b1173f4c 100644
--- a/R/importHumann.R
+++ b/R/importHumann.R
@@ -47,11 +47,11 @@
 #' 
 #' @seealso
 #' \code{\link[=importMetaPhlAn]{importMetaPhlAn}}
-#' \code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-#' \code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-#' \code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
 #' \code{\link[=importQIIME2]{importQIIME2}}
 #' \code{\link[=importMothur]{importMothur}}
+#' \code{\link[=convert]{convertFromDADA2}}
+#' \code{\link[=convert]{convertFromPhyloseq}}
+#' \code{\link[=convert]{convertFromBIOM}}
 #'
 #' @export
 #' @author Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
diff --git a/R/importMetaphlan.R b/R/importMetaphlan.R
index cd95b14fb..a3aca5022 100644
--- a/R/importMetaphlan.R
+++ b/R/importMetaphlan.R
@@ -60,11 +60,11 @@
 #' @name importMetaPhlAn
 #' @seealso
 #' \code{\link[=importHUMAnN]{importHUMAnN}}
-#' \code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-#' \code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-#' \code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
 #' \code{\link[=importQIIME2]{importQIIME2}}
 #' \code{\link[=importMothur]{importMothur}}
+#' \code{\link[=convert]{convertFromDADA2}}
+#' \code{\link[=convert]{convertFromPhyloseq}}
+#' \code{\link[=convert]{convertFromBIOM}}
 #'
 #' @export
 #' @author Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
diff --git a/R/importMothur.R b/R/importMothur.R
index 83e4256f2..f3c993a63 100644
--- a/R/importMothur.R
+++ b/R/importMothur.R
@@ -35,9 +35,9 @@
 #'
 #' @name importMothur
 #' @seealso
-#' \code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-#' \code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-#' \code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
+#' \code{\link[=convert]{convertFromDADA2}}
+#' \code{\link[=convert]{convertFromPhyloseq}}
+#' \code{\link[=convert]{convertFromBIOM}}
 #' \code{\link[=importQIIME2]{importQIIME2}}
 #'
 #' @author Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
diff --git a/R/importQIIME2.R b/R/importQIIME2.R
index 2f65728c3..64a11e3a0 100644
--- a/R/importQIIME2.R
+++ b/R/importQIIME2.R
@@ -64,9 +64,9 @@
 #'
 #' @name importQIIME2
 #' @seealso
-#' \code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-#' \code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-#' \code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
+#' \code{\link[=convert]{convertFromDADA2}}
+#' \code{\link[=convert]{convertFromPhyloseq}}
+#' \code{\link[=convert]{convertFromBIOM}}
 #' \code{\link[=importMothur]{importMothur}}
 #'
 #' @export
diff --git a/R/makeTreeSummarizedExperimentFromPhyloseq.R b/R/makeTreeSummarizedExperimentFromPhyloseq.R
deleted file mode 100644
index 15e64b916..000000000
--- a/R/makeTreeSummarizedExperimentFromPhyloseq.R
+++ /dev/null
@@ -1,90 +0,0 @@
-#' Coerce a \code{phyloseq} object to a \code{TreeSummarizedExperiment}
-#'
-#' \code{makeTreeSEFromPhyloseq} converts \code{phyloseq}
-#' objects into \code{TreeSummarizedExperiment} objects.
-#'
-#' All data stored in a \code{phyloseq} object is transferred.
-#'
-#' @param x a \code{phyloseq} object
-#'
-#' @return An object of class \code{TreeSummarizedExperiment}
-#'
-#' @importFrom S4Vectors SimpleList DataFrame make_zero_col_DFrame
-#' @importFrom SummarizedExperiment colData colData<-
-#'
-#' @export
-#'
-#' @name makeTreeSEFromPhyloseq
-#' @seealso
-#' \code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-#' \code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
-#' \code{\link[=importQIIME2]{importQIIME2}}
-#' \code{\link[=importMothur]{importMothur}}
-#'
-#' @examples
-#' if (requireNamespace("phyloseq")) {
-#'     data(GlobalPatterns, package="phyloseq")
-#'     makeTreeSEFromPhyloseq(GlobalPatterns)
-#'     data(enterotype, package="phyloseq")
-#'     makeTreeSEFromPhyloseq(enterotype)
-#'     data(esophagus, package="phyloseq")
-#'     makeTreeSEFromPhyloseq(esophagus)
-#' }
-makeTreeSEFromPhyloseq <- function(x) {
-    # input check
-    .require_package("phyloseq")
-    if(!is(x,"phyloseq")){
-        stop("'x' must be a 'phyloseq' object")
-    }
-    #
-    # Get the assay
-    counts <- x@otu_table@.Data
-    # Check the orientation, and transpose if necessary
-    if( !x@otu_table@taxa_are_rows ){
-        counts <- t(counts)
-    }
-    # Create a list of assays
-    assays <- SimpleList(counts = counts)
-    
-    if(!is.null(x@tax_table@.Data)){
-        rowData <- DataFrame(data.frame(x@tax_table@.Data))
-    } else{
-        rowData <- S4Vectors::make_zero_col_DFrame(nrow(assays$counts))
-        rownames(rowData) <- rownames(assays$counts)
-    }
-    if(!is.null(x@sam_data)){
-        colData <- DataFrame(data.frame(x@sam_data))
-    } else{
-        colData <- S4Vectors::make_zero_col_DFrame(ncol(assays$counts))
-        rownames(colData) <- colnames(assays$counts)
-    }
-    if(!is.null(x@phy_tree)){
-        rowTree <- x@phy_tree
-    } else {
-        rowTree <- NULL
-    }
-    if (!is.null(x@refseq)) {
-        referenceSeq <- x@refseq
-    } else {
-        referenceSeq <- NULL
-    }
-    TreeSummarizedExperiment(assays = assays,
-                            rowData = rowData,
-                            colData = colData,
-                            rowTree = rowTree,
-                            referenceSeq = referenceSeq)
-}
-
-####################### makeTreeSummarizedExperimentFromPhyloseq #######################
-#' @rdname makeTreeSEFromPhyloseq
-#' @export
-setGeneric("makeTreeSummarizedExperimentFromPhyloseq", signature = c("x"),
-    function(x)
-        standardGeneric("makeTreeSummarizedExperimentFromPhyloseq"))
-
-#' @rdname makeTreeSEFromPhyloseq
-#' @export
-setMethod("makeTreeSummarizedExperimentFromPhyloseq", signature = c(x = "ANY"),
-    function(x){
-        makeTreeSEFromPhyloseq(x)
-    })
diff --git a/R/makephyloseqFromTreeSummarizedExperiment.R b/R/makephyloseqFromTreeSummarizedExperiment.R
deleted file mode 100644
index 908a7052b..000000000
--- a/R/makephyloseqFromTreeSummarizedExperiment.R
+++ /dev/null
@@ -1,279 +0,0 @@
-#' Create a phyloseq object from a TreeSummarizedExperiment object
-#'
-#' This function creates a phyloseq object from a TreeSummarizedExperiment
-#' object. By using \code{assay.type}, it is possible to specify which table
-#' from \code{assay} is added to the phyloseq object.
-#'
-#' @param x a \code{TreeSummarizedExperiment} object
-#'
-#' @param assay.type A single character value for selecting the
-#'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}} to be
-#'   included in the phyloseq object that is created. 
-#'   (By default: \code{assay.type = "counts"})
-#'   
-#' @param assay_name a single \code{character} value for specifying which
-#'   assay to use for calculation.
-#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
-#'   will be disabled.)
-#'   
-#' @param tree.name a single \code{character} value for specifying which
-#'   tree will be included in the phyloseq object that is created, 
-#'   (By default: \code{tree.name = "phylo"})
-#'   
-#' @param tree_name Deprecated. Use \code{tree.name} instead.
-#'
-#' @param ... additional arguments
-#'
-#' @details
-#' \code{makePhyloseqFromTreeSE} is used for creating a
-#' phyloseq object from TreeSummarizedExperiment object.
-#'
-#' @return
-#' An object of class \code{Phyloseq} object.
-#'
-#' @name makePhyloseqFromTreeSE
-#' @export
-#'
-#' @author Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
-#'
-#' @examples
-#' # Get tse object
-#' data(GlobalPatterns)
-#' tse <- GlobalPatterns
-#'
-#' # Create a phyloseq object from it
-#' phy <- makePhyloseqFromTreeSE(tse)
-#' phy
-#'
-#' # By default the chosen table is counts, but if there are other tables,
-#' # they can be chosen with assay.type.
-#'
-#' # Counts relative abundances table
-#' tse <- transformAssay(tse, method = "relabundance")
-#' phy2 <- makePhyloseqFromTreeSE(tse, assay.type = "relabundance")
-#' phy2
-NULL
-
-#' @rdname makePhyloseqFromTreeSE
-#' @export
-setGeneric("makePhyloseqFromTreeSE", signature = c("x"),
-           function(x, ...)
-               standardGeneric("makePhyloseqFromTreeSE"))
-
-
-#' @rdname makePhyloseqFromTreeSE
-#' @export
-setMethod("makePhyloseqFromTreeSE",
-          signature = c(x = "SummarizedExperiment"),
-    function(x, assay.type = "counts", assay_name = NULL, ...){
-        # Input check
-        .require_package("phyloseq")
-        # Check that tse do not have zero rows
-        if(!all(dim(x) > 0)){
-            stop("'x' contains zero rows. 'x' can not be converted
-                 to a phyloseq object.",
-                 call. = FALSE)
-        }
-
-        if (!is.null(assay_name)) {
-            .Deprecated(old="assay_name", new="assay.type", "Now assay_name is deprecated. Use assay.type instead.")
-        }
-	
-        # Check assay.type
-        .check_assay_present(assay.type, x)
-        
-        # phyloseq object requires nonduplicated rownames. If there are 
-        # duplicated rownames, they are converted so that they are unique
-        if( any(duplicated(rownames(x))) ){
-            rownames(x) <- getTaxonomyLabels(x)
-        }
-        # List of arguments
-        args = list()
-        # Gets the abundance data from assay, and converts it to otu_table
-        otu_table <- as.matrix(assay(x, assay.type))
-        otu_table <- phyloseq::otu_table(otu_table, taxa_are_rows = TRUE)
-        # Adds to the list
-        args[["otu_table"]] <- otu_table
-
-        # If rowData includes information
-        if(!( length(rowData(x)[,taxonomyRanks(x)]) == 0 ||
-              is.null((rowData(x)[,taxonomyRanks(x)])) )){
-            # Converts taxonomy table to characters if it's not already
-            rowData(x) <- DataFrame(lapply(rowData(x), as.character))
-            # Gets the taxonomic data from rowData, and converts it to tax_table
-            tax_table <- as.matrix(rowData(x)[,taxonomyRanks(x),drop=FALSE])
-            tax_table <- phyloseq::tax_table(tax_table)
-            # Adds to the list
-            args[["tax_table"]] <- tax_table
-        }
-        
-        # If colData includes information
-        if(!( length(colData(x)) == 0 || is.null(ncol(colData(x))) )){
-            # Gets the feature_data from colData and converts it to sample_data
-            sample_data <- as.data.frame(colData(x))
-            sample_data <- phyloseq::sample_data(sample_data)
-            # Adds to the list
-            args[["sample_data"]] <- sample_data
-        }
-        
-        # Creates a phyloseq object
-        phyloseq <- do.call(phyloseq::phyloseq, args)
-        return(phyloseq)
-    }
-)
-
-#' @rdname makePhyloseqFromTreeSE
-#' @export
-setMethod("makePhyloseqFromTreeSE",
-          signature = c(x = "TreeSummarizedExperiment"),
-    function(x, tree.name = tree_name, tree_name = "phylo", ...){
-        # If rowTrees exist, check tree.name
-        if( length(x@rowTree) > 0 ){
-            .check_rowTree_present(tree.name, x)
-            # Subset the data based on the tree
-            x <- x[ rowLinks(x)$whichTree == tree.name, ]
-            add_phy_tree <- TRUE
-        } else{
-            add_phy_tree <- FALSE
-        }
-        #
-        
-        # phyloseq and tree objects require nonduplicated rownames. If there are 
-        # duplicated rownames, they are converted so that they are unique
-        if( any(duplicated(rownames(x))) ){
-            rownames(x) <- getTaxonomyLabels(x)
-        }
-        # Gets otu_table object from the function above this, if tse contains
-        # only abundance table.
-        # Otherwise, gets a phyloseq object with otu_table, and tax_table
-        # and/or sample_data
-        obj <- callNextMethod()
-        # List of arguments
-        args = list()
-        # Adds to the list of arguments, if 'obj' is not a phyloseq object
-        # i.e. is an otu_table
-        if(!is(obj,"phyloseq")){
-            # Adds otu_table to the list
-            args[["otu_table"]] <- obj
-        }
-        
-        # Add phylogenetic tree
-        if( add_phy_tree ){
-            phy_tree <- .get_rowTree_for_phyloseq(x, tree.name)
-            # If the object is a phyloseq object, adds phy_tree to it
-            if(is(obj,"phyloseq")){
-                phyloseq::phy_tree(obj) <- phy_tree
-            } else{
-                # Adds to the list
-                args[["phy_tree"]] <- phy_tree
-            }
-        }
-        
-        # If referenceSeq has information, stores it to refseq and converts is
-        # to phyloseq's refseq.
-        if( !is.null(referenceSeq(x)) ){
-            # Get referenceSeqs
-            refseq <- .get_referenceSeq_for_phyloseq(x, ...)
-            # IF refSeq passed the test, add it
-            if( !is.null(refseq) ){
-                # Convert it to phyloseq object
-                refseq <- phyloseq::refseq(refseq)
-                # If the object is a phyloseq object, adds refseq to it
-                if(is(obj,"phyloseq")){
-                    obj <- phyloseq::merge_phyloseq(obj, refseq)
-                } else{
-                    # Adds to the list
-                    args[["refseq"]] <- refseq
-                }
-            }
-        }
-        
-        # If 'obj' is not a phyloseq object, creates one.
-        if(!is(obj,"phyloseq")){
-            # Creates a phyloseq object
-            phyloseq <- do.call(phyloseq::phyloseq, args)
-        } else{
-            phyloseq <- obj
-        }
-        phyloseq
-    }
-)
-
-################### makePhyloseqFromTreeSummarizedExperiment ###################
-#' @rdname makePhyloseqFromTreeSE
-#' @export
-setGeneric("makePhyloseqFromTreeSummarizedExperiment", signature = c("x"),
-    function(x, ...)
-        standardGeneric("makePhyloseqFromTreeSummarizedExperiment"))
-
-#' @rdname makePhyloseqFromTreeSE
-#' @export
-setMethod("makePhyloseqFromTreeSummarizedExperiment", signature = c(x = "ANY"),
-        function(x, ...){
-            makePhyloseqFromTreeSE(x, ...)
-    })
-
-################################ HELP FUNCTIONS ################################
-# If tips do not match with rownames, prune the tree
-.get_x_with_pruned_tree <- function(x, tree.name){
-    # Get rowLinks
-    row_links <- rowLinks(x)
-    # Gets node labels
-    node_labs <- row_links[ , "nodeLab"]
-    # Prunes the tree
-    tree_pruned <- ape::keep.tip(rowTree(x), node_labs)
-    # Replace tip labels with corresponding rownames
-    tree_pruned$tip.label <- rownames(x)
-    # Assigns the pruned tree back to TSE object
-    rowTree(x) <- tree_pruned
-    warning("Tips of rowTree are renamed to match rownames.", call. = FALSE)
-    return(x)
-}
-
-# In phyloseq, tips and rownames must match
-.get_rowTree_for_phyloseq <- function(x, tree.name){
-    # Check if the rowTree's tips match with rownames:
-    # tips labels are found from rownames
-    if( any(!( rowTree(x, tree.name)$tip.label) %in% rownames(x)) ){
-        # If rowtree do not match, tree is pruned
-        x <- .get_x_with_pruned_tree(x, tree.name)
-    }
-    # Get rowTree
-    phy_tree <- rowTree(x, tree.name)
-    # Convert rowTree to phyloseq object
-    phy_tree <- phyloseq::phy_tree(phy_tree)
-        
-    return(phy_tree)
-}
-
-.get_referenceSeq_for_phyloseq <- function(x, referenceSeq = 1, ...){
-    # Get reference seqs
-    refSeqs <- referenceSeq(x)
-    # Is referenceSeq a list / does it contain multiple DNA sets
-    is_list <- is(refSeqs, "DNAStringSetList")
-    
-    # Take only one set, if it is a list
-    if( is_list ){
-        # Check referenceSeq
-        if( !( (.is_non_empty_string(referenceSeq) && referenceSeq %in% names(refSeqs)) ||
-            (.is_an_integer(referenceSeq) && (referenceSeq>0 && referenceSeq<=length(refSeqs))) )
-            ){
-            stop("'referenceSeq' must be a non-empty single character value or an integer ",
-                 "specifying the DNAStringSet from DNAStringSetList.",
-                 call. = FALSE)
-        }
-        # Get specified referenceSeq
-        refSeqs <- refSeqs[[referenceSeq]]
-        warning("Use 'referenceSeq' to specify DNA set from DNAStringSetList. ",
-                "Current choice is '", referenceSeq, "'.", 
-                call. = FALSE)
-    }
-    # Check if all rownames have referenceSeqs
-    if( !(all(rownames(x) %in% names(refSeqs)) &&
-        all(names(refSeqs) %in% rownames(x) )) ){
-        warning("referenceSeq does not match with rownames so they are discarded.",
-                call. = FALSE)
-        refSeqs <- NULL
-    }
-    return(refSeqs)
-}
\ No newline at end of file
diff --git a/man/convert.Rd b/man/convert.Rd
new file mode 100644
index 000000000..96c2627ae
--- /dev/null
+++ b/man/convert.Rd
@@ -0,0 +1,214 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/convertFromBIOM.R, R/convertFromDADA2.R,
+%   R/convertFromPhyloseq.R, R/convertToPhyloseq.R
+\name{convert}
+\alias{convert}
+\alias{importBIOM}
+\alias{convertFromBIOM}
+\alias{convertFromDADA2}
+\alias{convertFromPhyloseq}
+\alias{convertToPhyloseq}
+\alias{convertToPhyloseq,SummarizedExperiment-method}
+\alias{convertToPhyloseq,TreeSummarizedExperiment-method}
+\title{Converters}
+\usage{
+importBIOM(file, ...)
+
+convertFromBIOM(
+  obj,
+  prefix.rm = removeTaxaPrefixes,
+  removeTaxaPrefixes = FALSE,
+  rank.from.prefix = rankFromPrefix,
+  rankFromPrefix = FALSE,
+  artifact.rm = remove.artifacts,
+  remove.artifacts = FALSE,
+  ...
+)
+
+convertFromDADA2(...)
+
+convertFromPhyloseq(phy, ...)
+
+convertToPhyloseq(x, ...)
+
+\S4method{convertToPhyloseq}{SummarizedExperiment}(x, assay.type = "counts", assay_name = NULL, ...)
+
+\S4method{convertToPhyloseq}{TreeSummarizedExperiment}(x, tree.name = tree_name, tree_name = "phylo", ...)
+}
+\arguments{
+\item{file}{BIOM file location}
+
+\item{...}{Addional arguments. For \code{convertFromDADA2}, see
+\code{mergePairs} function for more details.}
+
+\item{obj}{BIOM object to be converted to a
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}}
+
+\item{prefix.rm}{\code{TRUE} or \code{FALSE}: Should
+taxonomic prefixes be removed? The prefixes is removed only from detected
+taxa columns meaning that \code{rank.from.prefix} should be enabled in the most cases.
+(default \code{prefix.rm = FALSE})}
+
+\item{removeTaxaPrefixes}{Deprecated. Use \code{prefix.rm} instead.}
+
+\item{rank.from.prefix}{\code{TRUE} or \code{FALSE}: If file does not have
+taxonomic ranks on feature table, should they be scraped from prefixes?
+(default \code{rank.from.prefix = FALSE})}
+
+\item{rankFromPrefix}{Deprecated.Use \code{rank.from.prefix} instead.}
+
+\item{artifact.rm}{\code{TRUE} or \code{FALSE}: If file have
+some taxonomic character naming artifacts, should they be removed.
+(default \code{artifact.rm = FALSE})}
+
+\item{remove.artifacts}{Deprecated. Use \code{artifact.rm} instead.}
+
+\item{phy}{a \code{phyloseq} object}
+
+\item{x}{a
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+object}
+
+\item{assay.type}{A single character value for selecting the
+\code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}} to be
+included in the phyloseq object that is created.
+(By default: \code{assay.type = "counts"})}
+
+\item{assay_name}{a single \code{character} value for specifying which
+assay to use for calculation.
+(Please use \code{assay.type} instead. At some point \code{assay_name}
+will be disabled.)}
+
+\item{tree.name}{a single \code{character} value for specifying which
+tree will be included in the phyloseq object that is created,
+(By default: \code{tree.name = "phylo"})}
+
+\item{tree_name}{a single \code{character} value for specifying which
+tree will be included in the phyloseq object that is created,
+(By default: \code{tree_name = "phylo"})
+\code{tree_name} will be deprecated. Use \code{tree.name} instead.}
+}
+\value{
+\code{importBIOM} returns an object of class
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+
+\code{convertFromBIOM} returns an object of class
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+
+\code{convertFromDADA2} returns an object of class
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+
+\code{convertFromPhyloseq} returns an object of class
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+
+\code{convertToPhyloseq} returns an object of class
+\code{\link[phyloseq:phyloseq-class]{phyloseq}}
+}
+\description{
+For convenience a few functions are available to convert BIOM, DADA2 and
+phyloseq objects to
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+objects and
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+objects to phyloseq objects.
+}
+\details{
+\code{convertFromBIOM} coerces a BIOM object to a
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+object.
+
+\code{importBIOM} loads a BIOM file and creates a
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+object from the BIOM object contained in the loaded file
+
+\code{convertFromDADA2} is a wrapper for the
+\code{mergePairs} function from the \code{dada2} package.
+A count matrix is constructed via
+\code{makeSequenceTable(mergePairs(...))} and rownames are dynamically
+created as \code{ASV(N)} with \code{N} from 1 to \code{nrow} of the count
+tables. The colnames and rownames from the output of \code{makeSequenceTable}
+are stored as \code{colnames} and in the \code{referenceSeq} slot of the
+\code{TreeSummarizedExperiment},respectively.
+
+\code{convertFromPhyloseq} converts \code{phyloseq}
+objects into
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}} objects.
+All data stored in a \code{phyloseq} object is transferred.
+
+\code{convertToPhyloseq} creates a phyloseq object from a
+\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
+object. By using \code{assay.type}, it is possible to specify which table
+from \code{assay} is added to the phyloseq object.
+}
+\examples{
+### Load and convert BIOM results to a TreeSE
+# Load biom file
+library(biomformat)
+biom_file <- system.file("extdata", "rich_dense_otu_table.biom",
+                         package = "biomformat")
+
+# Make TreeSE from biom file
+tse <- importBIOM(biom_file)
+
+# Make TreeSE from biom object
+biom_object <- biomformat::read_biom(biom_file)
+tse <- convertFromBIOM(biom_object)
+
+# Get taxonomyRanks from prefixes and remove prefixes
+tse <- importBIOM(biom_file,
+                    rank.from.prefix = TRUE,
+                    prefix.rm = TRUE)
+
+# Load another biom file
+biom_file <- system.file("extdata/testdata", "Aggregated_humanization2.biom",
+                         package = "mia")
+
+# Clean artifacts from taxonomic data
+tse <- importBIOM(biom_file,
+                    artifact.rm = TRUE)
+
+### Coerce DADA2 results to a TreeSE object
+if(requireNamespace("dada2")) {
+  fnF <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
+  fnR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
+  dadaF <- dada2::dada(fnF, selfConsist=TRUE)
+  dadaR <- dada2::dada(fnR, selfConsist=TRUE)
+
+  tse <- convertFromDADA2(dadaF, fnF, dadaR, fnR)
+  tse
+}
+
+### Coerce a phyloseq object to a TreeSE object
+if (requireNamespace("phyloseq")) {
+    data(GlobalPatterns, package="phyloseq")
+    convertFromPhyloseq(GlobalPatterns)
+    data(enterotype, package="phyloseq")
+    convertFromPhyloseq(enterotype)
+    data(esophagus, package="phyloseq")
+    convertFromPhyloseq(esophagus)
+}
+
+### Coerce a TreeSE object to a phyloseq object
+# Get tse object
+data(GlobalPatterns)
+tse <- GlobalPatterns
+
+# Create a phyloseq object from it
+phy <- convertToPhyloseq(tse)
+phy
+
+# By default the chosen table is counts, but if there are other tables,
+# they can be chosen with assay.type.
+
+# Counts relative abundances table
+tse <- transformAssay(tse, method = "relabundance")
+phy2 <- convertToPhyloseq(tse, assay.type = "relabundance")
+phy2
+}
+\seealso{
+\code{\link[=importQIIME2]{importQIIME2}}
+\code{\link[=importMothur]{importMothur}}
+}
+\author{
+Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
+}
diff --git a/man/deprecate.Rd b/man/deprecate.Rd
index 0518a4b51..a79180850 100644
--- a/man/deprecate.Rd
+++ b/man/deprecate.Rd
@@ -8,8 +8,14 @@
 \alias{addTaxonomyTree,SummarizedExperiment-method}
 \alias{taxonomyTree}
 \alias{taxonomyTree,SummarizedExperiment-method}
+\alias{makeTreeSummarizedExperimentFromPhyloseq}
+\alias{makeTreeSummarizedExperimentFromPhyloseq,ANY-method}
 \alias{mergeRows}
 \alias{mergeRows,SummarizedExperiment-method}
+\alias{makePhyloseqFromTreeSummarizedExperiment}
+\alias{makePhyloseqFromTreeSummarizedExperiment,ANY-method}
+\alias{makePhyloseqFromTreeSE}
+\alias{makePhyloseqFromTreeSE,ANY-method}
 \alias{mergeRows,TreeSummarizedExperiment-method}
 \alias{mergeCols}
 \alias{mergeCols,SummarizedExperiment-method}
@@ -25,6 +31,11 @@
 \alias{mergeFeaturesByRank,SingleCellExperiment-method}
 \alias{mergeFeaturesByPrevalence}
 \alias{mergeFeaturesByPrevalence,SummarizedExperiment-method}
+\alias{makeTreeSEFromBiom}
+\alias{makeTreeSummarizedExperimentFromBiom}
+\alias{makeTreeSEFromDADA2}
+\alias{makeTreeSummarizedExperimentFromDADA2}
+\alias{makeTreeSEFromPhyloseq}
 \alias{getExperimentCrossAssociation}
 \alias{getExperimentCrossAssociation,MultiAssayExperiment-method}
 \alias{getExperimentCrossAssociation,SummarizedExperiment-method}
@@ -119,10 +130,22 @@ taxonomyTree(x, ...)
 
 \S4method{taxonomyTree}{SummarizedExperiment}(x, ...)
 
+makeTreeSummarizedExperimentFromPhyloseq(x)
+
+\S4method{makeTreeSummarizedExperimentFromPhyloseq}{ANY}(x)
+
 mergeRows(x, ...)
 
 \S4method{mergeRows}{SummarizedExperiment}(x, ...)
 
+makePhyloseqFromTreeSummarizedExperiment(x, ...)
+
+\S4method{makePhyloseqFromTreeSummarizedExperiment}{ANY}(x, ...)
+
+makePhyloseqFromTreeSE(x, ...)
+
+\S4method{makePhyloseqFromTreeSE}{ANY}(x, ...)
+
 \S4method{mergeRows}{TreeSummarizedExperiment}(x, ...)
 
 mergeCols(x, ...)
@@ -153,6 +176,16 @@ mergeFeaturesByPrevalence(x, ...)
 
 \S4method{mergeFeaturesByPrevalence}{SummarizedExperiment}(x, ...)
 
+makeTreeSEFromBiom(...)
+
+makeTreeSummarizedExperimentFromBiom(...)
+
+makeTreeSEFromDADA2(...)
+
+makeTreeSummarizedExperimentFromDADA2(...)
+
+makeTreeSEFromPhyloseq(x)
+
 getExperimentCrossAssociation(x, ...)
 
 \S4method{getExperimentCrossAssociation}{MultiAssayExperiment}(x, ...)
@@ -314,9 +347,7 @@ perSampleDominantTaxa(x, ...)
 \S4method{perSampleDominantTaxa}{SummarizedExperiment}(x, ...)
 }
 \arguments{
-\item{x}{A
-\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
-object.}
+\item{x}{an object}
 
 \item{...}{Additional parameters. See dedicated function.}
 }
diff --git a/man/importHUMAnN.Rd b/man/importHUMAnN.Rd
index 603953cc3..331d722fd 100644
--- a/man/importHUMAnN.Rd
+++ b/man/importHUMAnN.Rd
@@ -68,11 +68,11 @@ microbial communities with bioBakery 3. \emph{eLife}. 10:e65088.
 }
 \seealso{
 \code{\link[=importMetaPhlAn]{importMetaPhlAn}}
-\code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-\code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-\code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
 \code{\link[=importQIIME2]{importQIIME2}}
 \code{\link[=importMothur]{importMothur}}
+\code{\link[=convert]{convertFromDADA2}}
+\code{\link[=convert]{convertFromPhyloseq}}
+\code{\link[=convert]{convertFromBIOM}}
 }
 \author{
 Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
diff --git a/man/importMetaPhlAn.Rd b/man/importMetaPhlAn.Rd
index 5b7c1f0d8..d4cd6bf70 100644
--- a/man/importMetaPhlAn.Rd
+++ b/man/importMetaPhlAn.Rd
@@ -90,11 +90,11 @@ and strain-level profiling of diverse microbial communities with bioBakery 3.
 }
 \seealso{
 \code{\link[=importHUMAnN]{importHUMAnN}}
-\code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-\code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-\code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
 \code{\link[=importQIIME2]{importQIIME2}}
 \code{\link[=importMothur]{importMothur}}
+\code{\link[=convert]{convertFromDADA2}}
+\code{\link[=convert]{convertFromPhyloseq}}
+\code{\link[=convert]{convertFromBIOM}}
 }
 \author{
 Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
diff --git a/man/importMothur.Rd b/man/importMothur.Rd
index 5e8561b02..e1ecdc7ea 100644
--- a/man/importMothur.Rd
+++ b/man/importMothur.Rd
@@ -72,9 +72,9 @@ tse
 \url{https://mothur.org/wiki/design_file/}
 }
 \seealso{
-\code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-\code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-\code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
+\code{\link[=convert]{convertFromDADA2}}
+\code{\link[=convert]{convertFromPhyloseq}}
+\code{\link[=convert]{convertFromBIOM}}
 \code{\link[=importQIIME2]{importQIIME2}}
 }
 \author{
diff --git a/man/importQIIME2.Rd b/man/importQIIME2.Rd
index eb63b21e8..b3658160b 100644
--- a/man/importQIIME2.Rd
+++ b/man/importQIIME2.Rd
@@ -149,9 +149,9 @@ microbiome data science using QIIME 2. Nature Biotechnology 37: 852–857.
 \url{https://qiime2.org}
 }
 \seealso{
-\code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-\code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-\code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
+\code{\link[=convert]{convertFromDADA2}}
+\code{\link[=convert]{convertFromPhyloseq}}
+\code{\link[=convert]{convertFromBIOM}}
 \code{\link[=importMothur]{importMothur}}
 }
 \author{
diff --git a/man/makePhyloseqFromTreeSE.Rd b/man/makePhyloseqFromTreeSE.Rd
deleted file mode 100644
index 37f472be3..000000000
--- a/man/makePhyloseqFromTreeSE.Rd
+++ /dev/null
@@ -1,73 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/makephyloseqFromTreeSummarizedExperiment.R
-\name{makePhyloseqFromTreeSE}
-\alias{makePhyloseqFromTreeSE}
-\alias{makePhyloseqFromTreeSE,SummarizedExperiment-method}
-\alias{makePhyloseqFromTreeSE,TreeSummarizedExperiment-method}
-\alias{makePhyloseqFromTreeSummarizedExperiment}
-\alias{makePhyloseqFromTreeSummarizedExperiment,ANY-method}
-\title{Create a phyloseq object from a TreeSummarizedExperiment object}
-\usage{
-makePhyloseqFromTreeSE(x, ...)
-
-\S4method{makePhyloseqFromTreeSE}{SummarizedExperiment}(x, assay.type = "counts", assay_name = NULL, ...)
-
-\S4method{makePhyloseqFromTreeSE}{TreeSummarizedExperiment}(x, tree.name = tree_name, tree_name = "phylo", ...)
-
-makePhyloseqFromTreeSummarizedExperiment(x, ...)
-
-\S4method{makePhyloseqFromTreeSummarizedExperiment}{ANY}(x, ...)
-}
-\arguments{
-\item{x}{a \code{TreeSummarizedExperiment} object}
-
-\item{...}{additional arguments}
-
-\item{assay.type}{A single character value for selecting the
-\code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}} to be
-included in the phyloseq object that is created.
-(By default: \code{assay.type = "counts"})}
-
-\item{assay_name}{a single \code{character} value for specifying which
-assay to use for calculation.
-(Please use \code{assay.type} instead. At some point \code{assay_name}
-will be disabled.)}
-
-\item{tree.name}{a single \code{character} value for specifying which
-tree will be included in the phyloseq object that is created,
-(By default: \code{tree.name = "phylo"})}
-
-\item{tree_name}{Deprecated. Use \code{tree.name} instead.}
-}
-\value{
-An object of class \code{Phyloseq} object.
-}
-\description{
-This function creates a phyloseq object from a TreeSummarizedExperiment
-object. By using \code{assay.type}, it is possible to specify which table
-from \code{assay} is added to the phyloseq object.
-}
-\details{
-\code{makePhyloseqFromTreeSE} is used for creating a
-phyloseq object from TreeSummarizedExperiment object.
-}
-\examples{
-# Get tse object
-data(GlobalPatterns)
-tse <- GlobalPatterns
-
-# Create a phyloseq object from it
-phy <- makePhyloseqFromTreeSE(tse)
-phy
-
-# By default the chosen table is counts, but if there are other tables,
-# they can be chosen with assay.type.
-
-# Counts relative abundances table
-tse <- transformAssay(tse, method = "relabundance")
-phy2 <- makePhyloseqFromTreeSE(tse, assay.type = "relabundance")
-phy2
-}
-\author{
-Leo Lahti and Tuomas Borman. Contact: \url{microbiome.github.io}
-}
diff --git a/man/makeTreeSEFromBiom.Rd b/man/makeTreeSEFromBiom.Rd
deleted file mode 100644
index 6fb71bc8f..000000000
--- a/man/makeTreeSEFromBiom.Rd
+++ /dev/null
@@ -1,95 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/makeTreeSummarizedExperimentFromBiom.R
-\name{makeTreeSEFromBiom}
-\alias{makeTreeSEFromBiom}
-\alias{importBIOM}
-\alias{makeTreeSummarizedExperimentFromBiom}
-\title{Loading a biom file}
-\usage{
-importBIOM(file, ...)
-
-makeTreeSEFromBiom(
-  x,
-  prefix.rm = removeTaxaPrefixes,
-  removeTaxaPrefixes = FALSE,
-  rank.from.prefix = rankFromPrefix,
-  rankFromPrefix = FALSE,
-  artifact.rm = remove.artifacts,
-  remove.artifacts = FALSE,
-  ...
-)
-
-makeTreeSummarizedExperimentFromBiom(x, ...)
-}
-\arguments{
-\item{file}{biom file location}
-
-\item{...}{additional arguments
-\itemize{
-\item \code{patter}: \code{character} value specifying artifacts
-to be removed. If \code{patterns = "auto"}, special characters
-are removed. (default: \code{pattern = "auto"})
-}}
-
-\item{x}{object of type \code{\link[biomformat:read_biom]{biom}}}
-
-\item{prefix.rm}{\code{TRUE} or \code{FALSE}: Should
-taxonomic prefixes be removed? The prefixes is removed only from detected
-taxa columns meaning that \code{rank.from.prefix} should be enabled in the most cases.
-(default \code{prefix.rm = FALSE})}
-
-\item{removeTaxaPrefixes}{Deprecated. Use \code{prefix.rm} instead.}
-
-\item{rank.from.prefix}{\code{TRUE} or \code{FALSE}: If file does not have
-taxonomic ranks on feature table, should they be scraped from prefixes?
-(default \code{rank.from.prefix = FALSE})}
-
-\item{rankFromPrefix}{Deprecated.Use \code{rank.from.prefix} instead.}
-
-\item{artifact.rm}{\code{TRUE} or \code{FALSE}: If file have
-some taxonomic character naming artifacts, should they be removed.
-(default \code{artifact.rm = FALSE})}
-
-\item{remove.artifacts}{Deprecated. Use \code{artifact.rm} instead.}
-}
-\value{
-An object of class
-\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
-}
-\description{
-For convenience a few functions are available to convert data from a
-\sQuote{biom} file or object into a
-\code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{TreeSummarizedExperiment}}
-}
-\examples{
-# Load biom file
-library(biomformat)
-biom_file <- system.file("extdata", "rich_dense_otu_table.biom",
-                         package = "biomformat")
-
-# Make TreeSE from biom file
-tse <- importBIOM(biom_file)
-
-# Make TreeSE from biom object
-biom_object <- biomformat::read_biom(biom_file)
-tse <- makeTreeSEFromBiom(biom_object)
-
-# Get taxonomyRanks from prefixes and remove prefixes
-tse <- importBIOM(biom_file,
-                    rank.from.prefix = TRUE,
-                    prefix.rm = TRUE)
-
-# Load another biom file
-biom_file <- system.file("extdata/testdata", "Aggregated_humanization2.biom",
-                         package = "mia")
-
-# Clean artifacts from taxonomic data
-tse <- importBIOM(biom_file,
-                    artifact.rm = TRUE)
-}
-\seealso{
-\code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-\code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
-\code{\link[=importQIIME2]{importQIIME2}}
-\code{\link[=importMothur]{importMothur}}
-}
diff --git a/man/makeTreeSEFromDADA2.Rd b/man/makeTreeSEFromDADA2.Rd
deleted file mode 100644
index f01459426..000000000
--- a/man/makeTreeSEFromDADA2.Rd
+++ /dev/null
@@ -1,47 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/makeTreeSummarizedExperimentFromDADA2.R
-\name{makeTreeSEFromDADA2}
-\alias{makeTreeSEFromDADA2}
-\alias{makeTreeSummarizedExperimentFromDADA2}
-\title{Coerce \sQuote{DADA2} results to \code{TreeSummarizedExperiment}}
-\usage{
-makeTreeSEFromDADA2(...)
-
-makeTreeSummarizedExperimentFromDADA2(...)
-}
-\arguments{
-\item{...}{See \code{mergePairs} function for
-more details.}
-}
-\value{
-An object of class \code{TreeSummarizedExperiment}
-}
-\description{
-\code{makeTreeSEFromDADA2} is a wrapper for the
-\code{mergePairs} function from the \code{dada2} package.
-}
-\details{
-A count matrix is constructed via \code{makeSequenceTable(mergePairs(...))}
-and rownames are dynamically created as \code{ASV(N)} with \code{N} from
-1 to \code{nrow} of the count tables. The colnames and rownames from the
-output of \code{makeSequenceTable} are stored as \code{colnames} and in the
-\code{referenceSeq} slot of the \code{TreeSummarizedExperiment},
-respectively.
-}
-\examples{
-if(requireNamespace("dada2")) {
-  fnF <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
-  fnR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
-  dadaF <- dada2::dada(fnF, selfConsist=TRUE)
-  dadaR <- dada2::dada(fnR, selfConsist=TRUE)
-
-  tse <- makeTreeSEFromDADA2(dadaF, fnF, dadaR, fnR)
-  tse
-}
-}
-\seealso{
-\code{\link[=makeTreeSEFromPhyloseq]{makeTreeSEFromPhyloseq}}
-\code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-\code{\link[=importQIIME2]{importQIIME2}}
-\code{\link[=importMothur]{importMothur}}
-}
diff --git a/man/makeTreeSEFromPhyloseq.Rd b/man/makeTreeSEFromPhyloseq.Rd
deleted file mode 100644
index f629642e7..000000000
--- a/man/makeTreeSEFromPhyloseq.Rd
+++ /dev/null
@@ -1,43 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/makeTreeSummarizedExperimentFromPhyloseq.R
-\name{makeTreeSEFromPhyloseq}
-\alias{makeTreeSEFromPhyloseq}
-\alias{makeTreeSummarizedExperimentFromPhyloseq}
-\alias{makeTreeSummarizedExperimentFromPhyloseq,ANY-method}
-\title{Coerce a \code{phyloseq} object to a \code{TreeSummarizedExperiment}}
-\usage{
-makeTreeSEFromPhyloseq(x)
-
-makeTreeSummarizedExperimentFromPhyloseq(x)
-
-\S4method{makeTreeSummarizedExperimentFromPhyloseq}{ANY}(x)
-}
-\arguments{
-\item{x}{a \code{phyloseq} object}
-}
-\value{
-An object of class \code{TreeSummarizedExperiment}
-}
-\description{
-\code{makeTreeSEFromPhyloseq} converts \code{phyloseq}
-objects into \code{TreeSummarizedExperiment} objects.
-}
-\details{
-All data stored in a \code{phyloseq} object is transferred.
-}
-\examples{
-if (requireNamespace("phyloseq")) {
-    data(GlobalPatterns, package="phyloseq")
-    makeTreeSEFromPhyloseq(GlobalPatterns)
-    data(enterotype, package="phyloseq")
-    makeTreeSEFromPhyloseq(enterotype)
-    data(esophagus, package="phyloseq")
-    makeTreeSEFromPhyloseq(esophagus)
-}
-}
-\seealso{
-\code{\link[=makeTreeSEFromBiom]{makeTreeSEFromBiom}}
-\code{\link[=makeTreeSEFromDADA2]{makeTreeSEFromDADA2}}
-\code{\link[=importQIIME2]{importQIIME2}}
-\code{\link[=importMothur]{importMothur}}
-}
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 06be0afd4..dc286b536 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -12,14 +12,11 @@ reference:
   - transformAssay
 - subtitle: Data loading
 - contents:
-  - makeTreeSummarizedExperimentFromPhyloseq
-  - makeTreeSummarizedExperimentFromDADA2
-  - importBIOM
+  - convert
   - importQIIME2
   - importMothur
   - importMetaPhlAn
   - importHUMAnN
-  - makePhyloseqFromTreeSummarizedExperiment
 - title: Taxonomic data
   contents:
   - taxonomyRanks
diff --git a/tests/testthat/test-4IO.R b/tests/testthat/test-4IO.R
index 3f1be3da0..ce37e2b81 100644
--- a/tests/testthat/test-4IO.R
+++ b/tests/testthat/test-4IO.R
@@ -7,7 +7,7 @@ test_that("Importing biom files yield SummarizedExperiment objects", {
     expect_s4_class(me, "SummarizedExperiment")
     # load from object
     x1 <- biomformat::read_biom(rich_dense_file)
-    me2 <- makeTreeSEFromBiom(x1)
+    me2 <- convertFromBIOM(x1)
     expect_s4_class(me2, "SummarizedExperiment")
     expect_equal(dim(me), dim(me2))
     expect_equal(rowData(me), rowData(me2))
@@ -16,11 +16,11 @@ test_that("Importing biom files yield SummarizedExperiment objects", {
         system.file("extdata/testdata/Aggregated_humanization2.biom",
                     package="mia")
     )
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm = FALSE,
-                                rank.from.prefix = FALSE,
-                                artifact.rm = TRUE,
-                                pattern = "\"")
+    tse <- convertFromBIOM(biom_object,
+                            prefix.rm = FALSE,
+                            rank.from.prefix = FALSE,
+                            artifact.rm = TRUE,
+                            pattern = "\"")
     # Testing no prefixes removed
     expect_true(rowData(tse) %>%
                     apply(2,grepl,pattern="sk__|([dkpcofgs]+)__") %>%
@@ -34,53 +34,57 @@ test_that("Importing biom files yield SummarizedExperiment objects", {
     expect_false(apply(rowData(tse), 2, grepl, pattern="^\"") %>% all())
     
     # Testing prefixes removed
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm=TRUE,
-                                rank.from.prefix=TRUE,
-                                artifact.rm = TRUE,
-                                pattern = "\"")
+    tse <- convertFromBIOM(biom_object,
+                           prefix.rm=TRUE,
+                           rank.from.prefix=TRUE,
+                           artifact.rm = TRUE,
+                           pattern = "\"")
     expect_false(rowData(tse) %>%
                     apply(2,grepl,pattern="sk__|([dkpcofgs]+)__") %>%
                     all())
     
     # Testing parsing taxonomy ranks from prefixes
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm=FALSE,
-                                rank.from.prefix=TRUE,
-                                artifact.rm = TRUE,
-                                pattern = "\"")
+    tse <- convertFromBIOM(biom_object,
+                              prefix.rm=FALSE,
+                              rank.from.prefix=TRUE,
+                              artifact.rm = TRUE,
+                              pattern = "\"")
     expect_true(
         sapply(tolower(colnames(rowData(tse))),
                 function(x) x %in% TAXONOMY_RANKS) %>% all())
     
     # Testing the artifact.rm, the original artifact in the biom file 
     # is '\"', as a test we rather try remove a non existing pattern.
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm=FALSE,
-                                rank.from.prefix=FALSE,
-                                artifact.rm = TRUE,
-                                pattern = "\\*|\\?")
+    tse <- convertFromBIOM(biom_object,
+                              prefix.rm=FALSE,
+                              rank.from.prefix=FALSE,
+                              artifact.rm = TRUE,
+                              pattern = "\\*|\\?")
     # with wrong pattern artifact not cleaned
     expect_true(apply(rowData(tse), 2, grepl, pattern="\"") %>% any())
     # Testing the artifact.rm, with the value 'auto' to automatically 
     # detect the artifact and remove it (in our case the artifact is '\"').
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm=FALSE,
-                                rank.from.prefix=FALSE,
-                                artifact.rm = TRUE)
+    tse <- convertFromBIOM(biom_object,
+                              prefix.rm=FALSE,
+                              rank.from.prefix=FALSE,
+                              artifact.rm = TRUE)
     # Checking if 'auto' has detected and cleaned the artifact
     expect_false(apply(rowData(tse), 2, grepl, pattern="\"") %>% any())
     # Testing the artifact.rm, with the value NULL to not detect or clean 
     # anything.
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm=FALSE,
-                                rank.from.prefix=FALSE,
-                                artifact.rm = FALSE)
+    tse <- convertFromBIOM(biom_object,
+                              prefix.rm=FALSE,
+                              rank.from.prefix=FALSE,
+                              artifact.rm = FALSE)
     # Checking if the '\"' artifact still exists.
     expect_true(apply(rowData(tse), 2, grepl, pattern="\"") %>% any())
     
     # General final test
-    tse <- makeTreeSEFromBiom(biom_object,
+    tse <- convertFromBIOM(biom_object,
+                              prefix.rm=TRUE,
+                              rank.from.prefix=TRUE,
+                              artifact.rm = TRUE)
+    tse <- convertFromBIOM(biom_object,
                                 prefix.rm=TRUE,
                                 rank.from.prefix=TRUE,
                                 artifact.rm = TRUE)
@@ -100,10 +104,10 @@ test_that("Importing biom files yield SummarizedExperiment objects", {
         system.file("extdata", "rich_dense_otu_table.biom",
                     package = "biomformat")
     )
-    tse <- makeTreeSEFromBiom(biom_object,
-                                prefix.rm=TRUE,
-                                rank.from.prefix=TRUE,
-                                artifact.rm = TRUE)
+    tse <- convertFromBIOM(biom_object,
+                              prefix.rm=TRUE,
+                              rank.from.prefix=TRUE,
+                              artifact.rm = TRUE)
     # check if taxa prefixes removed
     expect_false(rowData(tse) %>%
                     apply(2,grepl,pattern="sk__|([dkpcofgs]+)__") %>%
@@ -117,20 +121,20 @@ test_that("Importing biom files yield SummarizedExperiment objects", {
 test_that("Importing phyloseq objects yield TreeSummarizedExperiment objects", {
     skip_if_not_installed("phyloseq")
     data(GlobalPatterns, package="phyloseq")
-    me <- makeTreeSEFromPhyloseq(GlobalPatterns)
+    me <- convertFromPhyloseq(GlobalPatterns)
     expect_s4_class(me, "TreeSummarizedExperiment")
     expect_equal(dim(me),c(19216,26))
     data(enterotype, package="phyloseq")
-    me <- makeTreeSEFromPhyloseq(enterotype)
+    me <- convertFromPhyloseq(enterotype)
     expect_s4_class(me, "TreeSummarizedExperiment")
     expect_equal(dim(me),c(553,280))
     data(esophagus, package="phyloseq")
-    me <- makeTreeSEFromPhyloseq(esophagus)
+    me <- convertFromPhyloseq(esophagus)
     expect_s4_class(me, "TreeSummarizedExperiment")
     expect_equal(dim(me),c(58,3))
     esophagus2 <- esophagus
     phyloseq::otu_table(esophagus2) <- t(phyloseq::otu_table(esophagus))
-    me2 <- makeTreeSEFromPhyloseq(esophagus2)
+    me2 <- convertFromPhyloseq(esophagus2)
     expect_equal(me, me2)
 })
 
@@ -141,7 +145,7 @@ test_that("Importing dada2 objects yield TreeSummarizedExperiment objects", {
     dadaF <- dada2::dada(fnF, selfConsist=TRUE)
     dadaR <- dada2::dada(fnR, selfConsist=TRUE)
 
-    me <- makeTreeSEFromDADA2(dadaF, fnF, dadaR, fnR)
+    me <- convertFromDADA2(dadaF, fnF, dadaR, fnR)
     expect_s4_class(me, "TreeSummarizedExperiment")
 })
 
@@ -414,7 +418,7 @@ test_that("dimnames of feature table is identicle with meta data", {
 })
 
 
-test_that("makePhyloseqFromTreeSE", {
+test_that("convert TreeSE objects to phyloseq objects", {
 
     skip_if_not_installed("phyloseq")
 
@@ -422,7 +426,7 @@ test_that("makePhyloseqFromTreeSE", {
     data(GlobalPatterns, package="mia")
     tse <- GlobalPatterns
 
-    phy <- makePhyloseqFromTreeSE(GlobalPatterns)
+    phy <- convertToPhyloseq(GlobalPatterns)
 
     # Test that assay is in otu_table
     expect_equal(as.data.frame(phyloseq::otu_table(phy)@.Data), as.data.frame(assays(tse)$counts))
@@ -444,8 +448,8 @@ test_that("makePhyloseqFromTreeSE", {
     # Test with agglomeration that that pruning is done internally
     test1 <- agglomerateByRank(tse, rank = "Phylum")
     test2 <- agglomerateByRank(tse, rank = "Phylum", update.tree = TRUE)
-    test1_phy <- expect_warning(makePhyloseqFromTreeSE(test1))
-    test2_phy <- makePhyloseqFromTreeSE(test2)
+    test1_phy <- expect_warning(convertToPhyloseq(test1))
+    test2_phy <- convertToPhyloseq(test2)
     
     expect_equal(length(phyloseq::phy_tree(test1_phy)$node), 
                 length(ape::keep.tip(rowTree(test1), rowLinks(test1)$nodeLab)$node))
@@ -456,21 +460,21 @@ test_that("makePhyloseqFromTreeSE", {
     # Check that everything works also with agglomerated data
     for (level in colnames(rowData(tse)) ){
         temp <- agglomerateByRank(tse, rank = level)
-        expect_warning(makePhyloseqFromTreeSE(temp))
+        expect_warning(convertToPhyloseq(temp))
     }
     
     tse2 <- tse
     # Concerts data frame to factors
     rowData(tse2) <- DataFrame(lapply(rowData(tse2), as.factor))
-    phy <- makePhyloseqFromTreeSE(tse)
-    phy2 <- makePhyloseqFromTreeSE(tse2)
+    phy <- convertToPhyloseq(tse)
+    phy2 <- convertToPhyloseq(tse2)
     expect_equal(phyloseq::tax_table(phy2), phyloseq::tax_table(phy))
     
     # TSE object
     data(esophagus, package="mia")
     tse <- esophagus
 
-    phy <- makePhyloseqFromTreeSE(tse, assay.type="counts")
+    phy <- convertToPhyloseq(tse, assay.type="counts")
 
     # Test that assay is in otu_table
     expect_equal(as.data.frame(phyloseq::otu_table(phy)@.Data), as.data.frame(assays(tse)$counts))
@@ -480,10 +484,10 @@ test_that("makePhyloseqFromTreeSE", {
     
     # Test that merging objects lead to correct phyloseq
     tse <- mergeSEs(GlobalPatterns, esophagus, assay.type="counts", missing.values = 0)
-    pseq <- makePhyloseqFromTreeSE(tse, assay.type="counts")
+    pseq <- convertToPhyloseq(tse, assay.type="counts")
     
     tse_compare <- tse[ rownames(GlobalPatterns), ]
-    pseq_compare <- makePhyloseqFromTreeSE(tse_compare, assay.type="counts")
+    pseq_compare <- convertToPhyloseq(tse_compare, assay.type="counts")
     
     expect_equal(phyloseq::otu_table(pseq), phyloseq::otu_table(pseq_compare))
 })
diff --git a/tests/testthat/test-5Unifrac.R b/tests/testthat/test-5Unifrac.R
index bf86df8b1..126c7cac0 100644
--- a/tests/testthat/test-5Unifrac.R
+++ b/tests/testthat/test-5Unifrac.R
@@ -47,7 +47,6 @@ test_that("Unifrac beta diversity", {
     unifrac_rbiom <- as.matrix(rbiom::unifrac(assay(tse), weighted = TRUE,
                                               rowTree(tse)))
     expect_equal(unifrac_mia, unifrac_rbiom, tolerance = 1e-3)
-    
     # Test with merged object with multiple trees. runUnifrac takes subset of
     # data based on provided tree.
     tse <- mergeSEs(GlobalPatterns, esophagus, assay.type="counts", missing.values = 0)
@@ -63,7 +62,6 @@ test_that("Unifrac beta diversity", {
     unifrac_rbiom <- as.matrix(rbiom::unifrac(assay(tse_ref), weighted = TRUE,
                                               rowTree(tse_ref)))
     expect_equal(unifrac_mia, unifrac_rbiom, tolerance = 1e-3)
-    
     # Test the function with agglomerated data. runUnifrac renames rownames
     # based on tips and links to them. Then it also prunes the tree so that
     # rows are in tips.
diff --git a/vignettes/mia.Rmd b/vignettes/mia.Rmd
index 687f0794d..8c2da84af 100644
--- a/vignettes/mia.Rmd
+++ b/vignettes/mia.Rmd
@@ -280,12 +280,12 @@ data(esophagus, package = "phyloseq")
 
 ```{r}
 esophagus
-esophagus <- makeTreeSEFromPhyloseq(esophagus)
+esophagus <- convertFromPhyloseq(esophagus)
 esophagus
 ```
 
 For more details have a look at the man page, for examples 
-`?makeTreeSEFromPhyloseq`.
+`?convert`.
 
 ## General wrapper functions