diff --git a/.Rbuildignore b/.Rbuildignore
index 5d3a89f0..6e3409c0 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -19,3 +19,4 @@
 ^codemeta\.json$
 ^codecov\.yml$
 ^\.out.R
+^CONTRIBUTING.md$
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7469f2d0..c31debad 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -12,10 +12,11 @@ phangorn is an open source project, maintained by people who care. We are not di
 [website]: https://KlausVigo.github.io/phangorn
 [citation]: https://KlausVigo.github.io/phangorn/authors.html
 [email]: mailto:klaus.schliep@gmail.com
-
+<!--
 ## Code of conduct
 
 Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
+-->
 
 ## How you can contribute
 
diff --git a/NAMESPACE b/NAMESPACE
index 49763310..54a1de4b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -198,6 +198,7 @@ export(optim.parsimony)
 export(optim.pml)
 export(pace)
 export(parsimony)
+export(parsimony_edgelength)
 export(path.dist)
 export(phyDat)
 export(phyDat2MultipleAlignment)
diff --git a/R/distTree.R b/R/distTree.R
index 7d2e65c2..fb570362 100644
--- a/R/distTree.R
+++ b/R/distTree.R
@@ -305,9 +305,6 @@ designUnrooted2 <- function(tree, sparse = TRUE) {
 
 
 designTipDated <- function(tree, tip.dates, sparse=TRUE){
-  #, strict=TRUE
-  #if(!is.numeric(tip.dates)) browser()
-  #if(!length(tip.dates) >= Ntip(tree)) browser()
   stopifnot(is.numeric(tip.dates), length(tip.dates) >= Ntip(tree))
   nTip <- Ntip(tree)
   tmp <- function(n){
@@ -367,7 +364,7 @@ designConstrained <- function(tree, sparse=TRUE, tip.dates=NULL,
 #' @export
 nnls.tree <- function(dm, tree, method=c("unrooted", "ultrametric", "tipdated"),
           rooted=NULL, trace=1, weight=NULL, balanced=FALSE, tip.dates=NULL,
-          constraint=NULL) {
+          calibration=NULL) {
   method <- match.arg(method, c("unrooted", "ultrametric", "tipdated"))
   if(has.singles(tree)) tree <- collapse.singles(tree)
   if (is.rooted(tree) && method == "unrooted") tree <- unroot(tree)
diff --git a/R/fitch64.R b/R/fitch64.R
index 9954b5fe..779c5469 100644
--- a/R/fitch64.R
+++ b/R/fitch64.R
@@ -89,7 +89,7 @@ random.addition <- function (data, tree=NULL, method = "fitch")
     tree$edge <- edge
     remaining <- sample(setdiff(label, tree$tip.label))
     tree$tip.label <- c(tree$tip.label, remaining)
-    tree <- relabel(tree, label)
+    tree <- checkLabels(tree, label)
     remaining <- match(remaining, label)
   }
 
diff --git a/R/joint_ASR.R b/R/joint_ASR.R
index cac60932..740f4eaf 100644
--- a/R/joint_ASR.R
+++ b/R/joint_ASR.R
@@ -139,26 +139,44 @@ joint_sankoff <- function(tree, data, cost=NULL){
 }
 
 
-# alternative to acctran(tree, data)
+#' Assign edge length to tree
+#'
+#' \code{parsimony_edgelength} and \code{acctran} assign edge length to a tree where
+#' the edge length is the number of mutations. \code{parsimony_edgelengths}
+#' assigns edge lengths using a joint reconstruction based on the sankoff
+#' algorithm. Ties are broken at random and trees can be multifurating.
+#' \code{acctran} is based on the fitch algorithm and is faster. However trees
+#' need to be bifurcating and ties are split.
+#' @param tree a tree, i.e. an object of class pml
+#' @param data an object of class phyDat
+#' @return a tree with edge length.
+#' @export
+parsimony_edgelength <- function(tree, data){
+  if(inherits(tree, "phylo")) return(count_mutations(tree, data))
+  if(inherits(tree, "multiPhylo")) {
+    res <- lapply(tree, count_mutations, data=data)
+    class(res) <- "multiPhylo"
+    return(res)
+  }
+  NULL
+}
+
+
 count_mutations <- function(tree, data){
-  site <- "pscore"
   tree <- reorder(tree, "postorder")
   data <- data[tree$tip.label]
   tree_tmp <- makeNodeLabel(tree)
   anc <- joint_sankoff(tree_tmp, data)
+#  ind <-   length(data)+seq_along(anc)
+#  data[ind] <- anc
+#  names(dat[ind]) <- names(anc)
   dat <- rbind(data, anc)
-  nr <- attr(data, "nr")
   l <- length(dat)
-  fun <- function(x, site="pscore", nr){
-    if(site=="pscore") return(f$pscore(x))
-    sites <- f$sitewise_pscore(x)
-    sites[seq_len(nr)]
-  }
   f <- init_fitch(dat, FALSE, FALSE, m=2L)
   el <- numeric(nrow(tree$edge))
   for(i in seq_along(el)){
     edge_i <-  matrix(c(l+1L, l+1L, tree$edge[i,]), 2, 2)
-    el[i] <- fun(edge_i, site, nr)
+    el[i] <- f$pscore(edge_i)
   }
   tree$edge.length <- el
   tree
diff --git a/R/plotAnc.R b/R/plotAnc.R
index 265eed3a..02280a34 100644
--- a/R/plotAnc.R
+++ b/R/plotAnc.R
@@ -41,7 +41,7 @@ getTransition <- function(scheme, levels){
 #' @param \dots Further arguments passed to or from other methods.
 #' @returns \code{plotAnc} returns silently x.
 #' @author Klaus Schliep \email{klaus.schliep@@gmail.com}
-#' @seealso \code{\link{ancestral.pml}}, \code{\link[ape]{plot.phylo}},
+#' @seealso \code{\link{anc_pml}}, \code{\link[ape]{plot.phylo}},
 #' \code{\link[ape]{image.DNAbin}}, \code{\link[ape]{image.AAbin}}
 #' \code{\link[ggseqlogo]{ggseqlogo}}, \code{\link[ape]{edgelabels}}
 #' @keywords plot
diff --git a/man/designTree.Rd b/man/designTree.Rd
index 30a62297..98b40c74 100644
--- a/man/designTree.Rd
+++ b/man/designTree.Rd
@@ -14,7 +14,7 @@ designTree(tree, method = "unrooted", sparse = FALSE, tip.dates = NULL,
 
 nnls.tree(dm, tree, method = c("unrooted", "ultrametric", "tipdated"),
   rooted = NULL, trace = 1, weight = NULL, balanced = FALSE,
-  tip.dates = NULL)
+  tip.dates = NULL, calibration = NULL)
 
 nnls.phylo(x, dm, method = "unrooted", trace = 0, ...)
 
diff --git a/man/parsimony_edgelength.Rd b/man/parsimony_edgelength.Rd
new file mode 100644
index 00000000..89067657
--- /dev/null
+++ b/man/parsimony_edgelength.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/joint_ASR.R
+\name{parsimony_edgelength}
+\alias{parsimony_edgelength}
+\title{Assign edge length to tree}
+\usage{
+parsimony_edgelength(tree, data)
+}
+\arguments{
+\item{tree}{a tree, i.e. an object of class pml}
+
+\item{data}{an object of class phyDat}
+}
+\value{
+a tree with edge length.
+}
+\description{
+\code{parsimony_edgelength} and \code{acctran} assign edge length to a tree where
+the edge length is the number of mutations. \code{parsimony_edgelengths}
+assigns edge lengths using a joint reconstruction based on the sankoff
+algorithm. Ties are broken at random and trees can be multifurating.
+\code{acctran} is based on the fitch algorithm and is faster. However trees
+need to be bifurcating and ties are split.
+}
diff --git a/man/plot.ancestral.Rd b/man/plot.ancestral.Rd
index eff6544c..d23f18f5 100644
--- a/man/plot.ancestral.Rd
+++ b/man/plot.ancestral.Rd
@@ -91,7 +91,7 @@ add_mutations(anc_aa, adj = c(.5, -0.3), col=2)
 
 }
 \seealso{
-\code{\link{ancestral.pml}}, \code{\link[ape]{plot.phylo}},
+\code{\link{anc_pml}}, \code{\link[ape]{plot.phylo}},
 \code{\link[ape]{image.DNAbin}}, \code{\link[ape]{image.AAbin}}
 \code{\link[ggseqlogo]{ggseqlogo}}, \code{\link[ape]{edgelabels}}
 }