diff --git a/DESCRIPTION b/DESCRIPTION
index 6980a5a..c92fd9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -58,6 +58,7 @@ Collate:
     'GenomicBreaks.R'
     'HKY85_distance.R'
     'JC69_distance.R'
+    'JC69_distance_allseq.R'
     'K80_distance.R'
     'K80_gap_distance.R'
     'P_distance.R'
diff --git a/NAMESPACE b/NAMESPACE
index fa6d439..55b4ff3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -13,6 +13,7 @@ export(GCproportion)
 export(GOC)
 export(HKY85_distance)
 export(JC69_distance)
+export(JC69_distance_allseq)
 export(K80_distance)
 export(K80_gap_distance)
 export(P_distance)
diff --git a/R/JC69_distance_allseq.R b/R/JC69_distance_allseq.R
new file mode 100644
index 0000000..f0b94d9
--- /dev/null
+++ b/R/JC69_distance_allseq.R
@@ -0,0 +1,62 @@
+#' Variation of the Jukes-Cantor 1969 distance
+#'
+#' The Jukes-Cantor 1969 (JC69) distance corrects the p-distance for multiple substitutions, 
+#' providing an estimate of evolutionary distance that is proportional to time under the model.
+#' The correction is based on the proportion of nucleotide differences, typically obtained 
+#' by counting mismatches in the alignment matrix.
+#' Here, the Jukes-Cantor equation remains unchanged, but the definition of which base pairs 
+#' are considered different is modified.
+#'
+#' In this function, the fraction of nucleotides that are different incorporates not only the 
+#' mismatches from the alignment matrix but also the base pairs that are left unaligned.
+#' The rationale is that these unaligned base pairs likely differ primarily because of point 
+#' substitutions and should therefore be treated as mismatches that were not detected by the aligner. 
+#' In fact, the aligner can only spot mismatches in regions where the proportion of matches is high enough for alignment.
+#'
+#' Notice that gaps are usually not included in the Jukes-Cantor distance, including in this variation, 
+#' because they are generally considered to result from indels (insertions and deletions that affect multiple 
+#' nucleotides at once), whereas the Jukes-Cantor model is based only on point substitutions. 
+#' Therefore, including regions that were likely affected by large evolutionary events, such as gaps caused by indels, 
+#' would incorrectly inflate a distance calculated under a model in which only one position is mutated at a time.
+#'
+#' @references Jukes, T.H. & Cantor, C.R. (1969). "Evolution of protein molecules." In *Mammalian Protein Metabolism* (pp. 21–132). Academic Press.
+#'
+#' @param gb A [`GBreaks`] object.
+#' @param m  A matrix of **counts** for bases of the _target_ genome to be aligned to bases on the _query_ genome.
+#' @param adjust_p A boolean flag. If `TRUE`, the distance is scaled between `0` and `0.75` to ensure the logarithm stays positive.
+#'
+#' @family Alignment statistics
+#' @family Similarity indexes
+#'
+#' @author Priscila Biller
+#'
+#' @returns Returns a numeric value representing the evolutionary distance between two genomes. The greater the value, the more genetically different the genomes are.
+#'
+#' @examples
+#'
+#' # Only the sequence length is used from the GenomicBreaks object.
+#' gb       <- GRanges(c("Ref:100-35000000:+"))
+#' gb$query <- GRanges(c("Que:1100-35000500:+"))
+#' d <- JC69_distance_allseq(gb, exampleSubstitutionMatrix)
+#'
+#' @export
+JC69_distance_allseq <- function(gb, m, adjust_p=FALSE) {
+  
+  if(length(gb) == 0) return(numeric(0))
+  if (all(m == 0)) return(NA)
+
+  # Gets the smallest sequence length.
+  totBps <- min(sum(guessSeqLengths(gb)),sum(guessSeqLengths(gb$query)))
+
+  # Matrix of aligned base pairs, excluding gaps.
+  non_gap    <- c("A", "C", "G", "T")
+  m_non_gap  <- m[non_gap, non_gap]
+
+  aligned    <- sum(m)                     # Total aligned base pairs.
+  matches    <- sum(diag(m_non_gap))       # Matches.
+  mismatches <- sum(m_non_gap)-matches     # Mismatches.
+  gaps       <- aligned-matches-mismatches # Gaps
+  unaligned  <- totBps - aligned           # Total unaligned base pairs.
+
+  JC69_distance(mismatches+unaligned, tot=totBps-gaps, adjust_p=adjust_p)
+} 
diff --git a/man/F81_distance.Rd b/man/F81_distance.Rd
index 58873d7..ce3fe36 100644
--- a/man/F81_distance.Rd
+++ b/man/F81_distance.Rd
@@ -43,6 +43,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
@@ -56,6 +57,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/GCequilibrium.Rd b/man/GCequilibrium.Rd
index 13d7ad0..6a78c25 100644
--- a/man/GCequilibrium.Rd
+++ b/man/GCequilibrium.Rd
@@ -53,6 +53,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/GCpressure.Rd b/man/GCpressure.Rd
index eef219e..f9f5225 100644
--- a/man/GCpressure.Rd
+++ b/man/GCpressure.Rd
@@ -38,6 +38,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/GCproportion.Rd b/man/GCproportion.Rd
index b00ffda..1a32ce9 100644
--- a/man/GCproportion.Rd
+++ b/man/GCproportion.Rd
@@ -31,6 +31,7 @@ Other Alignment statistics:
 \code{\link[=GCpressure]{GCpressure()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/GOC.Rd b/man/GOC.Rd
index cc07c5e..126a3eb 100644
--- a/man/GOC.Rd
+++ b/man/GOC.Rd
@@ -61,6 +61,7 @@ Other Similarity indexes:
 \code{\link[=F81_distance]{F81_distance()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/HKY85_distance.Rd b/man/HKY85_distance.Rd
index b46716e..1f9664e 100644
--- a/man/HKY85_distance.Rd
+++ b/man/HKY85_distance.Rd
@@ -66,6 +66,7 @@ Other Alignment statistics:
 \code{\link[=GCpressure]{GCpressure()}},
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
@@ -79,6 +80,7 @@ Other Similarity indexes:
 \code{\link[=F81_distance]{F81_distance()}},
 \code{\link[=GOC]{GOC()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/JC69_distance.Rd b/man/JC69_distance.Rd
index 2af2303..ba27ca1 100644
--- a/man/JC69_distance.Rd
+++ b/man/JC69_distance.Rd
@@ -41,6 +41,7 @@ Other Alignment statistics:
 \code{\link[=GCpressure]{GCpressure()}},
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
@@ -54,6 +55,7 @@ Other Similarity indexes:
 \code{\link[=F81_distance]{F81_distance()}},
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/JC69_distance_allseq.Rd b/man/JC69_distance_allseq.Rd
new file mode 100644
index 0000000..f644b49
--- /dev/null
+++ b/man/JC69_distance_allseq.Rd
@@ -0,0 +1,93 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/JC69_distance_allseq.R
+\name{JC69_distance_allseq}
+\alias{JC69_distance_allseq}
+\title{Variation of the Jukes-Cantor 1969 distance}
+\usage{
+JC69_distance_allseq(gb, m, adjust_p = FALSE)
+}
+\arguments{
+\item{gb}{A \code{\link{GBreaks}} object.}
+
+\item{m}{A matrix of \strong{counts} for bases of the \emph{target} genome to be aligned to bases on the \emph{query} genome.}
+
+\item{adjust_p}{A boolean flag. If \code{TRUE}, the distance is scaled between \code{0} and \code{0.75} to ensure the logarithm stays positive.}
+}
+\value{
+Returns a numeric value representing the evolutionary distance between two genomes. The greater the value, the more genetically different the genomes are.
+}
+\description{
+The Jukes-Cantor 1969 (JC69) distance corrects the p-distance for multiple substitutions,
+providing an estimate of evolutionary distance that is proportional to time under the model.
+The correction is based on the proportion of nucleotide differences, typically obtained
+by counting mismatches in the alignment matrix.
+Here, the Jukes-Cantor equation remains unchanged, but the definition of which base pairs
+are considered different is modified.
+}
+\details{
+In this function, the fraction of nucleotides that are different incorporates not only the
+mismatches from the alignment matrix but also the base pairs that are left unaligned.
+The rationale is that these unaligned base pairs likely differ primarily because of point
+substitutions and should therefore be treated as mismatches that were not detected by the aligner.
+In fact, the aligner can only spot mismatches in regions where the proportion of matches is high enough for alignment.
+
+Notice that gaps are usually not included in the Jukes-Cantor distance, including in this variation,
+because they are generally considered to result from indels (insertions and deletions that affect multiple
+nucleotides at once), whereas the Jukes-Cantor model is based only on point substitutions.
+Therefore, including regions that were likely affected by large evolutionary events, such as gaps caused by indels,
+would incorrectly inflate a distance calculated under a model in which only one position is mutated at a time.
+}
+\examples{
+
+# Only the sequence length is used from the GenomicBreaks object.
+gb       <- GRanges(c("Ref:100-35000000:+"))
+gb$query <- GRanges(c("Que:1100-35000500:+"))
+d <- JC69_distance_allseq(gb, exampleSubstitutionMatrix)
+
+}
+\references{
+Jukes, T.H. & Cantor, C.R. (1969). "Evolution of protein molecules." In \emph{Mammalian Protein Metabolism} (pp. 21–132). Academic Press.
+}
+\seealso{
+Other Alignment statistics:
+\code{\link[=F81_distance]{F81_distance()}},
+\code{\link[=GCequilibrium]{GCequilibrium()}},
+\code{\link[=GCpressure]{GCpressure()}},
+\code{\link[=GCproportion]{GCproportion()}},
+\code{\link[=HKY85_distance]{HKY85_distance()}},
+\code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=K80_distance]{K80_distance()}},
+\code{\link[=K80_gap_distance]{K80_gap_distance()}},
+\code{\link[=P_distance]{P_distance()}},
+\code{\link[=T92_distance]{T92_distance()}},
+\code{\link[=TN93_distance]{TN93_distance()}},
+\code{\link{exampleSubstitutionMatrix}},
+\code{\link[=gapProportion]{gapProportion()}},
+\code{\link[=logDet_distance]{logDet_distance()}}
+
+Other Similarity indexes:
+\code{\link[=F81_distance]{F81_distance()}},
+\code{\link[=GOC]{GOC()}},
+\code{\link[=HKY85_distance]{HKY85_distance()}},
+\code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=K80_distance]{K80_distance()}},
+\code{\link[=K80_gap_distance]{K80_gap_distance()}},
+\code{\link[=P_distance]{P_distance()}},
+\code{\link[=T92_distance]{T92_distance()}},
+\code{\link[=TN93_distance]{TN93_distance()}},
+\code{\link[=breakpointGraphProperties]{breakpointGraphProperties()}},
+\code{\link[=correlation_index]{correlation_index()}},
+\code{\link[=inversionDistance]{inversionDistance()}},
+\code{\link[=inversionEstimate_BD]{inversionEstimate_BD()}},
+\code{\link[=karyotype_index]{karyotype_index()}},
+\code{\link[=logDet_distance]{logDet_distance()}},
+\code{\link[=slidingWindow]{slidingWindow()}},
+\code{\link[=strand_randomisation_index]{strand_randomisation_index()}},
+\code{\link[=synteny_index]{synteny_index()}},
+\code{\link[=tau_index]{tau_index()}}
+}
+\author{
+Priscila Biller
+}
+\concept{Alignment statistics}
+\concept{Similarity indexes}
diff --git a/man/K80_distance.Rd b/man/K80_distance.Rd
index 976c96d..1fbf512 100644
--- a/man/K80_distance.Rd
+++ b/man/K80_distance.Rd
@@ -33,6 +33,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
 \code{\link[=T92_distance]{T92_distance()}},
@@ -46,6 +47,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
 \code{\link[=T92_distance]{T92_distance()}},
diff --git a/man/K80_gap_distance.Rd b/man/K80_gap_distance.Rd
index 68c1d83..516c7f6 100644
--- a/man/K80_gap_distance.Rd
+++ b/man/K80_gap_distance.Rd
@@ -65,6 +65,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=P_distance]{P_distance()}},
 \code{\link[=T92_distance]{T92_distance()}},
@@ -78,6 +79,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=P_distance]{P_distance()}},
 \code{\link[=T92_distance]{T92_distance()}},
diff --git a/man/P_distance.Rd b/man/P_distance.Rd
index db94bf5..c8c4282 100644
--- a/man/P_distance.Rd
+++ b/man/P_distance.Rd
@@ -61,6 +61,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=T92_distance]{T92_distance()}},
@@ -74,6 +75,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=T92_distance]{T92_distance()}},
diff --git a/man/T92_distance.Rd b/man/T92_distance.Rd
index ff74792..124d206 100644
--- a/man/T92_distance.Rd
+++ b/man/T92_distance.Rd
@@ -38,6 +38,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
@@ -51,6 +52,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/TN93_distance.Rd b/man/TN93_distance.Rd
index 6e5586f..f397c01 100644
--- a/man/TN93_distance.Rd
+++ b/man/TN93_distance.Rd
@@ -54,6 +54,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
@@ -67,6 +68,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/breakpointGraphProperties.Rd b/man/breakpointGraphProperties.Rd
index e7e2308..568ea98 100644
--- a/man/breakpointGraphProperties.Rd
+++ b/man/breakpointGraphProperties.Rd
@@ -44,6 +44,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/correlation_index.Rd b/man/correlation_index.Rd
index 3e99b78..d5c6e1a 100644
--- a/man/correlation_index.Rd
+++ b/man/correlation_index.Rd
@@ -37,6 +37,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/exampleSubstitutionMatrix.Rd b/man/exampleSubstitutionMatrix.Rd
index 6cbc1a6..7fe7b3d 100644
--- a/man/exampleSubstitutionMatrix.Rd
+++ b/man/exampleSubstitutionMatrix.Rd
@@ -25,6 +25,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/gapProportion.Rd b/man/gapProportion.Rd
index e6e6483..48e82d0 100644
--- a/man/gapProportion.Rd
+++ b/man/gapProportion.Rd
@@ -44,6 +44,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/inversionDistance.Rd b/man/inversionDistance.Rd
index b5f1ab8..c134b70 100644
--- a/man/inversionDistance.Rd
+++ b/man/inversionDistance.Rd
@@ -55,6 +55,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/inversionEstimate_BD.Rd b/man/inversionEstimate_BD.Rd
index 0f486f6..b76aa76 100644
--- a/man/inversionEstimate_BD.Rd
+++ b/man/inversionEstimate_BD.Rd
@@ -92,6 +92,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/karyotype_index.Rd b/man/karyotype_index.Rd
index 80394f0..574dfc3 100644
--- a/man/karyotype_index.Rd
+++ b/man/karyotype_index.Rd
@@ -34,6 +34,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/logDet_distance.Rd b/man/logDet_distance.Rd
index 1ca5f36..7bae87a 100644
--- a/man/logDet_distance.Rd
+++ b/man/logDet_distance.Rd
@@ -72,6 +72,7 @@ Other Alignment statistics:
 \code{\link[=GCproportion]{GCproportion()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
@@ -85,6 +86,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/slidingWindow.Rd b/man/slidingWindow.Rd
index 923507f..41ce034 100644
--- a/man/slidingWindow.Rd
+++ b/man/slidingWindow.Rd
@@ -46,6 +46,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/strand_randomisation_index.Rd b/man/strand_randomisation_index.Rd
index 22a570d..44fb045 100644
--- a/man/strand_randomisation_index.Rd
+++ b/man/strand_randomisation_index.Rd
@@ -54,6 +54,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/synteny_index.Rd b/man/synteny_index.Rd
index bd69db6..79d3841 100644
--- a/man/synteny_index.Rd
+++ b/man/synteny_index.Rd
@@ -44,6 +44,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},
diff --git a/man/tau_index.Rd b/man/tau_index.Rd
index d97a01e..b685c96 100644
--- a/man/tau_index.Rd
+++ b/man/tau_index.Rd
@@ -59,6 +59,7 @@ Other Similarity indexes:
 \code{\link[=GOC]{GOC()}},
 \code{\link[=HKY85_distance]{HKY85_distance()}},
 \code{\link[=JC69_distance]{JC69_distance()}},
+\code{\link[=JC69_distance_allseq]{JC69_distance_allseq()}},
 \code{\link[=K80_distance]{K80_distance()}},
 \code{\link[=K80_gap_distance]{K80_gap_distance()}},
 \code{\link[=P_distance]{P_distance()}},