diff --git a/DESCRIPTION b/DESCRIPTION
index bd2b247..5d87247 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -38,7 +38,8 @@ Imports:
     tidytree,
     treeio,
     purrr,
-    yaml
+    yaml,
+    httr
 VignetteBuilder: knitr
 Collate: 
     'ConvenientTblTree.R'
@@ -64,6 +65,7 @@ Collate:
     'removeAssemblies.R'
     'resultFiles.R'
     'subMatrix.R'
+    'timeTree.R'
     'treeHeatMap.R'
     'visualizeTree.R'
     'zzz.R'
diff --git a/NAMESPACE b/NAMESPACE
index 9ac60ff..763a991 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -12,6 +12,8 @@ export(eog)
 export(extractValues)
 export(focalClade)
 export(formatStats)
+export(getDivergenceTime)
+export(getTimeline)
 export(makeMatrix)
 export(makeTidyTree)
 export(makeValueTibble)
@@ -28,54 +30,73 @@ export(thinByMin)
 export(treeHeatMap)
 export(visualizeTree)
 import(S7)
-importFrom(ape,as.phylo)
-importFrom(ape,cophenetic.phylo)
-importFrom(ape,prop.clades)
-importFrom(ape,prop.part)
-importFrom(dplyr,across)
-importFrom(dplyr,arrange)
-importFrom(dplyr,case_when)
-importFrom(dplyr,desc)
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,mutate)
-importFrom(dplyr,n)
-importFrom(dplyr,pull)
-importFrom(dplyr,summarise)
-importFrom(dplyr,summarize)
-importFrom(dplyr,sym)
-importFrom(dplyr,ungroup)
-importFrom(dplyr,where)
+importFrom(ape,
+  as.phylo,
+  cophenetic.phylo,
+  prop.clades,
+  prop.part
+)
+importFrom(dplyr,
+  across,
+  arrange,
+  case_when,
+  desc,
+  filter,
+  group_by,
+  mutate,
+  n,
+  pull,
+  summarise,
+  summarize,
+  sym,
+  ungroup,
+  where
+)
 importFrom(ggforce,geom_mark_ellipse)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,geom_errorbar)
-importFrom(ggplot2,geom_errorbarh)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,scale_color_manual)
-importFrom(ggplot2,scale_fill_manual)
-importFrom(ggplot2,scale_x_continuous)
-importFrom(ggplot2,scale_y_continuous)
-importFrom(ggplot2,theme_bw)
-importFrom(ggplot2,theme_minimal)
+importFrom(ggplot2,
+  aes,
+  geom_errorbar,
+  geom_errorbarh,
+  geom_point,
+  ggplot,
+  labs,
+  scale_color_manual,
+  scale_fill_manual,
+  scale_x_continuous,
+  scale_y_continuous,
+  theme_bw,
+  theme_minimal
+)
+importFrom(httr,
+  GET,
+  content
+)
 importFrom(pheatmap,pheatmap)
 importFrom(rlang,.data)
-importFrom(stats,as.dist)
-importFrom(stats,complete.cases)
-importFrom(stats,hclust)
-importFrom(stats,loess)
-importFrom(stats,mad)
-importFrom(stats,na.omit)
-importFrom(stats,predict)
-importFrom(stats,quantile)
-importFrom(stats,sd)
-importFrom(tidytree,as.treedata)
-importFrom(tidytree,as_tibble)
-importFrom(tidytree,child)
-importFrom(tidytree,offspring)
-importFrom(tidytree,tree_subset)
+importFrom(stats,
+  as.dist,
+  complete.cases,
+  hclust,
+  loess,
+  mad,
+  na.omit,
+  predict,
+  quantile,
+  sd
+)
+importFrom(tidytree,
+  as.treedata,
+  as_tibble,
+  child,
+  offspring,
+  tree_subset
+)
 importFrom(treeio,MRCA)
-importFrom(utils,read.delim)
-importFrom(yaml,read_yaml)
-importFrom(yaml,yaml.load)
+importFrom(utils,
+  read.csv,
+  read.delim
+)
+importFrom(yaml,
+  read_yaml,
+  yaml.load
+)
diff --git a/R/timeTree.R b/R/timeTree.R
new file mode 100644
index 0000000..be31c76
--- /dev/null
+++ b/R/timeTree.R
@@ -0,0 +1,93 @@
+#' Timeline - TimeTree
+#' 
+#' Fetches a list of divergence times of nodes in TimeTree from the specified taxon to the common ancestor of all cellular organisms. 
+#' 
+#' @param taxid An integer: The NCBI id of a taxon
+#'
+#' @return A dataframe in which each row corresponds to an ancestor. 
+#'         Each row contains the divergence time (`divtime`), its confidence interval 
+#'         (`divtimeCI_low` and `divtimeCI_high`), and additional information, 
+#'         including the scientific name (`name`) and taxonomic rank (`rank`).
+#'         If the divergence time is not found in the TimeTree database, it returns `NA`.
+#'
+#' @author Priscila Biller
+#'
+#' @examples
+#' \dontrun{
+#' getTimeline(9555)}
+#'
+#' @importFrom httr GET content
+#' @importFrom utils read.csv
+#'
+#' @export
+getTimeline <- function(taxid) {
+  timetreeBaseTimeline <- "http://timetree.temple.edu/api/timeline/"
+  # Example of request to the TimeTree's API: 
+  # - Request: http://timetree.temple.edu/api/timeline/9555
+  # - Answer from TimeTree: 
+  # ncbi-id,scientific_name,common_name,level,rank,summary_age,adjusted_age,ci_high,ci_low
+  # -1,unnamed,,46,unknown,1.1,1.1,1.48,0.72
+  # -1,unnamed,,45,unknown,1.27,1.36,1.97,0.56
+  # -1,unnamed,,44,unknown,1.27,1.58,1.97,0.56
+  # 9554,Papio,,43,genus,1.9,1.9,2.31,1.48
+  # -1,unnamed,,42,unknown,4.68,4.68,5.08,4.27
+  # ...
+  timetreeRequest  <- paste(timetreeBaseTimeline, taxid, sep="")
+  timetreeResponse <- GET(timetreeRequest)
+  lines  <- content(timetreeResponse, as="text", encoding="UTF-8")
+  header <- lines |> strsplit(split="\n", fixed=TRUE) |> (\(x) x[[1]][1])() |> strsplit(split = ",", fixed = TRUE) |> (\(x) x[[1]])() # First line: header; Other lines: data.
+  if(length(header) >= 8) {
+    df    <- read.csv(text=lines)
+    # In TimeTree there are two possibilities for the divergence time (here we go with "adjusted age"):
+    # - "Summary age" is the median of all studies.
+    # - "Adjusted age" is the adjusted time, computed in cases where a node is older than its parent in the global timetree reconstructed from individual timetrees.
+    df    <- df[ c("ncbi.id", "scientific_name", "rank", "adjusted_age", "ci_low",       "ci_high")]
+    names(df) <- c("NCBIid",  "name",            "rank", "divtime",     "divtimeCI_low", "divtimeCI_high")
+    df
+  } else {
+    NA
+  }
+}
+
+#' Divergence time - TimeTree
+#' 
+#' Retrieves the divergence time of two species via the TimeTree API.
+#' 
+#' @param taxid1 An integer: The NCBI id of one taxon
+#' @param taxid2 An integer: The NCBI id of the other taxon
+#'
+#' @return A list in which the first item is the divergence time (`divtime`),
+#'         and the last two items are the divergence time confidence interval 
+#'         (`divtimeCI_low` and `divtimeCI_high`).
+#'         If the divergence time is not found in the TimeTree database, it returns `NA`.
+#'
+#' @author Priscila Biller
+#'
+#' @examples
+#' \dontrun{
+#' getDivergenceTime(9555,9601)}
+#'
+#' @importFrom httr GET content
+#'
+#' @export
+getDivergenceTime <- function(taxid1, taxid2) {
+  timetreeBasePairwise <- "http://timetree.temple.edu/api/pairwise/"
+  # Example of request to the TimeTree's API: 
+  # - Request: http://timetree.temple.edu/api/pairwise/9555/9601
+  # - Answer from TimeTree: 
+  # taxon_a_id,taxon_b_id,scientific_name_a,scientific_name_b,all_total,precomputed_age,precomputed_ci_low,precomputed_ci_high,adjusted_age
+  # 9555,9601,Papio anubis,Pongo abelii,83,28.82,26.8,30.6,0
+  timetreeRequest  <- paste(timetreeBasePairwise, taxid1, "/", taxid2, sep="")
+  timetreeResponse <- GET(timetreeRequest)
+  lines <- content(timetreeResponse, as="text", encoding="UTF-8")
+  # Break the whole content into lines, and gets the second line (data).
+  lineData <- strsplit(lines, "\n", fixed = TRUE)[[1]][2] # First line: header; Second line: data.
+  # Break the line into data.
+  data <- strsplit(lineData, ",", fixed = TRUE)[[1]]
+  # Check if the request returned something valid.
+  if(length(data) >= 8) {
+    list(divtime=as.numeric(data[6]),divtimeCI_low=as.numeric(data[7]),divtimeCI_high=as.numeric(data[8]))
+  } else {
+    NA
+  }
+}
diff --git a/man/ConvenientTblTree.Rd b/man/ConvenientTblTree.Rd
index c072dea..a7d2050 100644
--- a/man/ConvenientTblTree.Rd
+++ b/man/ConvenientTblTree.Rd
@@ -1,12 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ConvenientTblTree.R
-\docType{data}
 \name{ConvenientTblTree}
 \alias{ConvenientTblTree}
 \title{Convenient tbl_trees}
-\format{
-An object of class \code{S7_S3_class} of length 3.
-}
 \usage{
 ConvenientTblTree
 }
@@ -23,4 +19,3 @@ order in which the nodes would be plotted.  This is needed by the
 \author{
 Charles Plessy
 }
-\keyword{datasets}
diff --git a/man/Haloarchaea.Rd b/man/Haloarchaea.Rd
index 98c52df..157c87d 100644
--- a/man/Haloarchaea.Rd
+++ b/man/Haloarchaea.Rd
@@ -32,7 +32,7 @@ Halo_FocalClades
 
 }
 \seealso{
-Other Lazy-loaded data: 
+Other Lazy-loaded data:
 \code{\link{oikData}}
 }
 \author{
diff --git a/man/MRCA_2D_plot.Rd b/man/MRCA_2D_plot.Rd
index 7249bb6..fbc358a 100644
--- a/man/MRCA_2D_plot.Rd
+++ b/man/MRCA_2D_plot.Rd
@@ -26,10 +26,10 @@ p + ggplot2::geom_point(
                color = focalClade))
 }
 \seealso{
-Other Plotting functions: 
-\code{\link{ellipsePlot}()},
-\code{\link{treeHeatMap}()},
-\code{\link{visualizeTree}()}
+Other Plotting functions:
+\code{\link[=ellipsePlot]{ellipsePlot()}},
+\code{\link[=treeHeatMap]{treeHeatMap()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/childSpecies.Rd b/man/childSpecies.Rd
index bb0da69..cbd5611 100644
--- a/man/childSpecies.Rd
+++ b/man/childSpecies.Rd
@@ -22,10 +22,10 @@ childSpecies(Halo_Tree, 7)
 
 }
 \seealso{
-Other Functions for trees: 
-\code{\link{extractValues}()},
-\code{\link{recordAncestor}()},
-\code{\link{subMatrix}()}
+Other Functions for trees:
+\code{\link[=extractValues]{extractValues()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=subMatrix]{subMatrix()}}
 }
 \author{
 Noa Brenner
diff --git a/man/ellipsePlot.Rd b/man/ellipsePlot.Rd
index 674378d..ae1bbb1 100644
--- a/man/ellipsePlot.Rd
+++ b/man/ellipsePlot.Rd
@@ -28,10 +28,10 @@ clade.
 ellipsePlot(Halo_DF |> averageResults())
 }
 \seealso{
-Other Plotting functions: 
-\code{\link{MRCA_2D_plot}()},
-\code{\link{treeHeatMap}()},
-\code{\link{visualizeTree}()}
+Other Plotting functions:
+\code{\link[=MRCA_2D_plot]{MRCA_2D_plot()}},
+\code{\link[=treeHeatMap]{treeHeatMap()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/eog.Rd b/man/eog.Rd
index 1a9ba14..245b41a 100644
--- a/man/eog.Rd
+++ b/man/eog.Rd
@@ -25,13 +25,13 @@ eog(Halo_Tree, Halo_FocalClades$Haloferax)
 
 }
 \seealso{
-Other Focal clade functions: 
-\code{\link{focalClade}()},
-\code{\link{recordAncestor}()},
-\code{\link{recordClades}()},
-\code{\link{subMatrix}()},
-\code{\link{subTree}()},
-\code{\link{visualizeTree}()}
+Other Focal clade functions:
+\code{\link[=focalClade]{focalClade()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=recordClades]{recordClades()}},
+\code{\link[=subMatrix]{subMatrix()}},
+\code{\link[=subTree]{subTree()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/extractValues.Rd b/man/extractValues.Rd
index ea2910d..2b3cb89 100644
--- a/man/extractValues.Rd
+++ b/man/extractValues.Rd
@@ -26,9 +26,9 @@ unique(Halo_Tree$parent) |> sort() |>
   purrr::set_names() |> sapply(extractValues, Halo_Tree, Halo_PercentDiff)
 }
 \seealso{
-Other Functions for trees: 
-\code{\link{childSpecies}()},
-\code{\link{recordAncestor}()},
-\code{\link{subMatrix}()}
+Other Functions for trees:
+\code{\link[=childSpecies]{childSpecies()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=subMatrix]{subMatrix()}}
 }
 \concept{Functions for trees}
diff --git a/man/focalClade.Rd b/man/focalClade.Rd
index 70ecc32..f56394e 100644
--- a/man/focalClade.Rd
+++ b/man/focalClade.Rd
@@ -29,13 +29,13 @@ Clades of interest to be plotted in color
 visualizeTree(Halo_Tree) + clades
 }
 \seealso{
-Other Focal clade functions: 
-\code{\link{eog}()},
-\code{\link{recordAncestor}()},
-\code{\link{recordClades}()},
-\code{\link{subMatrix}()},
-\code{\link{subTree}()},
-\code{\link{visualizeTree}()}
+Other Focal clade functions:
+\code{\link[=eog]{eog()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=recordClades]{recordClades()}},
+\code{\link[=subMatrix]{subMatrix()}},
+\code{\link[=subTree]{subTree()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/formatStats.Rd b/man/formatStats.Rd
index b000707..2eb32d4 100644
--- a/man/formatStats.Rd
+++ b/man/formatStats.Rd
@@ -33,8 +33,8 @@ exDataFrame <- formatStats(yamlFileData)
 exDataFrame[1:10,1:6]
 }
 \seealso{
-Other Data load functions: 
-\code{\link{resultFiles}()}
+Other Data load functions:
+\code{\link[=resultFiles]{resultFiles()}}
 }
 \author{
 Noah Brenner
diff --git a/man/getDivergenceTime.Rd b/man/getDivergenceTime.Rd
new file mode 100644
index 0000000..2aea125
--- /dev/null
+++ b/man/getDivergenceTime.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/timeTree.R
+\name{getDivergenceTime}
+\alias{getDivergenceTime}
+\title{Divergence time - TimeTree}
+\usage{
+getDivergenceTime(taxid1, taxid2)
+}
+\arguments{
+\item{taxid1}{An integer: The NCBI id of one taxon}
+
+\item{taxid2}{An integer: The NCBI id of the other taxon}
+}
+\value{
+A list in which the first item is the divergence time (\code{divtime}),
+and the last two items are the divergence time confidence interval
+(\code{divtimeCI_low} and \code{divtimeCI_high}).
+If the divergence time is not found in the TimeTree database, it returns \code{NA}.
+}
+\description{
+Retrieves the divergence time of two species via the TimeTree API.
+}
+\examples{
+\dontrun{
+getDivergenceTime(9555,9601)}
+
+}
+\author{
+Priscila Biller
+}
diff --git a/man/getTimeline.Rd b/man/getTimeline.Rd
new file mode 100644
index 0000000..b6a1af6
--- /dev/null
+++ b/man/getTimeline.Rd
@@ -0,0 +1,29 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/timeTree.R
+\name{getTimeline}
+\alias{getTimeline}
+\title{Timeline - TimeTree}
+\usage{
+getTimeline(taxid)
+}
+\arguments{
+\item{taxid}{An integer: The NCBI id of a taxon}
+}
+\value{
+A dataframe in which each row corresponds to an ancestor.
+Each row contains the divergence time (\code{divtime}), its confidence interval
+(\code{divtimeCI_low} and \code{divtimeCI_high}), and additional information,
+including the scientific name (\code{name}) and taxonomic rank (\code{rank}).
+If the divergence time is not found in the TimeTree database, it returns \code{NA}.
+}
+\description{
+Fetches a list of divergence times of nodes in TimeTree from the specified taxon to the common ancestor of all cellular organisms.
+}
+\examples{
+\dontrun{
+getTimeline(9555)}
+
+}
+\author{
+Priscila Biller
+}
diff --git a/man/oikData.Rd b/man/oikData.Rd
index 60fc056..5b47c94 100644
--- a/man/oikData.Rd
+++ b/man/oikData.Rd
@@ -28,7 +28,7 @@ by a beta version of the \url{https://nf-co.re/pairgenomealign} pipeline.
 oikData
 }
 \seealso{
-Other Lazy-loaded data: 
+Other Lazy-loaded data:
 \code{\link{Haloarchaea}}
 }
 \author{
diff --git a/man/recordAncestor.Rd b/man/recordAncestor.Rd
index 7a66889..f062363 100644
--- a/man/recordAncestor.Rd
+++ b/man/recordAncestor.Rd
@@ -23,18 +23,18 @@ recordAncestor(Halo_DF, Halo_Tree)$MRCA
 
 }
 \seealso{
-Other Functions for trees: 
-\code{\link{childSpecies}()},
-\code{\link{extractValues}()},
-\code{\link{subMatrix}()}
+Other Functions for trees:
+\code{\link[=childSpecies]{childSpecies()}},
+\code{\link[=extractValues]{extractValues()}},
+\code{\link[=subMatrix]{subMatrix()}}
 
-Other Focal clade functions: 
-\code{\link{eog}()},
-\code{\link{focalClade}()},
-\code{\link{recordClades}()},
-\code{\link{subMatrix}()},
-\code{\link{subTree}()},
-\code{\link{visualizeTree}()}
+Other Focal clade functions:
+\code{\link[=eog]{eog()}},
+\code{\link[=focalClade]{focalClade()}},
+\code{\link[=recordClades]{recordClades()}},
+\code{\link[=subMatrix]{subMatrix()}},
+\code{\link[=subTree]{subTree()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Noa Brenner
diff --git a/man/recordClades.Rd b/man/recordClades.Rd
index 9724c41..8d9857c 100644
--- a/man/recordClades.Rd
+++ b/man/recordClades.Rd
@@ -26,13 +26,13 @@ when it did not find it.
 recordClades(Halo_DF, Halo_FocalClades)
 }
 \seealso{
-Other Focal clade functions: 
-\code{\link{eog}()},
-\code{\link{focalClade}()},
-\code{\link{recordAncestor}()},
-\code{\link{subMatrix}()},
-\code{\link{subTree}()},
-\code{\link{visualizeTree}()}
+Other Focal clade functions:
+\code{\link[=eog]{eog()}},
+\code{\link[=focalClade]{focalClade()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=subMatrix]{subMatrix()}},
+\code{\link[=subTree]{subTree()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/resultFiles.Rd b/man/resultFiles.Rd
index 9483b17..f1fd465 100644
--- a/man/resultFiles.Rd
+++ b/man/resultFiles.Rd
@@ -30,8 +30,8 @@ system.file("extdata/yaml", package = "ScrambledTreeBuilder") |> resultFiles()
 
 }
 \seealso{
-Other Data load functions: 
-\code{\link{formatStats}()}
+Other Data load functions:
+\code{\link[=formatStats]{formatStats()}}
 }
 \author{
 Charles Plessy
diff --git a/man/subMatrix.Rd b/man/subMatrix.Rd
index 6d34d0c..e649ffb 100644
--- a/man/subMatrix.Rd
+++ b/man/subMatrix.Rd
@@ -40,18 +40,18 @@ subTree(Halo_Tree, 9) |> subMatrix(Halo_PercentDiff)
 
 }
 \seealso{
-Other Functions for trees: 
-\code{\link{childSpecies}()},
-\code{\link{extractValues}()},
-\code{\link{recordAncestor}()}
-
-Other Focal clade functions: 
-\code{\link{eog}()},
-\code{\link{focalClade}()},
-\code{\link{recordAncestor}()},
-\code{\link{recordClades}()},
-\code{\link{subTree}()},
-\code{\link{visualizeTree}()}
+Other Functions for trees:
+\code{\link[=childSpecies]{childSpecies()}},
+\code{\link[=extractValues]{extractValues()}},
+\code{\link[=recordAncestor]{recordAncestor()}}
+
+Other Focal clade functions:
+\code{\link[=eog]{eog()}},
+\code{\link[=focalClade]{focalClade()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=recordClades]{recordClades()}},
+\code{\link[=subTree]{subTree()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/subTree.Rd b/man/subTree.Rd
index 69ebffe..24dbe72 100644
--- a/man/subTree.Rd
+++ b/man/subTree.Rd
@@ -30,13 +30,13 @@ visualizeTree(subtree, subtree$node.orig)
 
 }
 \seealso{
-Other Focal clade functions: 
-\code{\link{eog}()},
-\code{\link{focalClade}()},
-\code{\link{recordAncestor}()},
-\code{\link{recordClades}()},
-\code{\link{subMatrix}()},
-\code{\link{visualizeTree}()}
+Other Focal clade functions:
+\code{\link[=eog]{eog()}},
+\code{\link[=focalClade]{focalClade()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=recordClades]{recordClades()}},
+\code{\link[=subMatrix]{subMatrix()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/treeHeatMap.Rd b/man/treeHeatMap.Rd
index 1d1e1a7..16ee2f1 100644
--- a/man/treeHeatMap.Rd
+++ b/man/treeHeatMap.Rd
@@ -30,10 +30,10 @@ treeHeatMap(Halo_PercentDiff, Halo_Tree, Halo_FocalClades)
 
 }
 \seealso{
-Other Plotting functions: 
-\code{\link{MRCA_2D_plot}()},
-\code{\link{ellipsePlot}()},
-\code{\link{visualizeTree}()}
+Other Plotting functions:
+\code{\link[=MRCA_2D_plot]{MRCA_2D_plot()}},
+\code{\link[=ellipsePlot]{ellipsePlot()}},
+\code{\link[=visualizeTree]{visualizeTree()}}
 }
 \author{
 Charles Plessy
diff --git a/man/visualizeTree.Rd b/man/visualizeTree.Rd
index 29d4185..665e195 100644
--- a/man/visualizeTree.Rd
+++ b/man/visualizeTree.Rd
@@ -42,18 +42,18 @@ visualizeTree(Halo_Tree, value = Halo_Tree$Scrambling_index)
 visualizeTree(Halo_Tree, "Scrambling_index") # same
 }
 \seealso{
-Other Focal clade functions: 
-\code{\link{eog}()},
-\code{\link{focalClade}()},
-\code{\link{recordAncestor}()},
-\code{\link{recordClades}()},
-\code{\link{subMatrix}()},
-\code{\link{subTree}()}
+Other Focal clade functions:
+\code{\link[=eog]{eog()}},
+\code{\link[=focalClade]{focalClade()}},
+\code{\link[=recordAncestor]{recordAncestor()}},
+\code{\link[=recordClades]{recordClades()}},
+\code{\link[=subMatrix]{subMatrix()}},
+\code{\link[=subTree]{subTree()}}
 
-Other Plotting functions: 
-\code{\link{MRCA_2D_plot}()},
-\code{\link{ellipsePlot}()},
-\code{\link{treeHeatMap}()}
+Other Plotting functions:
+\code{\link[=MRCA_2D_plot]{MRCA_2D_plot()}},
+\code{\link[=ellipsePlot]{ellipsePlot()}},
+\code{\link[=treeHeatMap]{treeHeatMap()}}
 }
 \author{
 Noah Brenner