diff --git a/R/nearest-methods.R b/R/nearest-methods.R
index baf0deb..024961a 100644
--- a/R/nearest-methods.R
+++ b/R/nearest-methods.R
@@ -173,7 +173,7 @@
 ###
 
 setMethod("precede", c("GenomicRanges", "GenomicRanges"),
-    function(x, subject, select = c("arbitrary", "all"), ignore.strand=FALSE)
+    function(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
     {
         select <- match.arg(select)
         .GenomicRanges_findPrecedeFollow(x, subject, select, ignore.strand, 
@@ -182,7 +182,7 @@ setMethod("precede", c("GenomicRanges", "GenomicRanges"),
 )
 
 setMethod("precede", c("GenomicRanges", "missing"),
-    function(x, subject, select = c("arbitrary", "all"), ignore.strand=FALSE)
+    function(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
     {
         select <- match.arg(select)
         .GenomicRanges_findPrecedeFollow(x, subject, select, ignore.strand, 
@@ -191,7 +191,7 @@ setMethod("precede", c("GenomicRanges", "missing"),
 )
 
 setMethod("follow", c("GenomicRanges", "GenomicRanges"),
-    function(x, subject, select = c("arbitrary", "all"), ignore.strand=FALSE)
+    function(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
     {
         select <- match.arg(select)
         .GenomicRanges_findPrecedeFollow(x, subject, select, ignore.strand, 
@@ -220,16 +220,16 @@ setMethod("follow", c("GenomicRanges", "missing"),
     m
 }
 
-.nearest <- function(x, subject, select, ignore.strand, ignoreSelf=FALSE)
+.nearest <- function(x, subject, select, algorithm,
+                     ignore.strand, ignoreSelf=FALSE)
 {
     ## overlapping ranges
     if (ignoreSelf) {
-        ol <- findOverlaps(x,
-                           select=select, ignore.strand=ignore.strand,
-                           ignoreSelf=TRUE)
+        ol <- findOverlaps(x, select=select, algorithm=algorithm,
+                           ignore.strand=ignore.strand, ignoreSelf=TRUE)
     } else {
-        ol <- findOverlaps(x, subject,
-                           select=select, ignore.strand=ignore.strand)
+        ol <- findOverlaps(x, subject, select=select, algorithm=algorithm,
+                           ignore.strand=ignore.strand)
     }
 
     if (select == "all") {
@@ -295,19 +295,22 @@ setMethod("follow", c("GenomicRanges", "missing"),
 
 
 setMethod("nearest", c("GenomicRanges", "GenomicRanges"),
-    function(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
+    function(x, subject, select=c("arbitrary", "all"),
+             algorithm=c("nclist", "intervaltree"), ignore.strand=FALSE)
     {
         select <- match.arg(select)
-        .nearest(x, subject, select=select, ignore.strand=ignore.strand)
+        .nearest(x, subject, select=select, algorithm=match.arg(algorithm),
+                 ignore.strand=ignore.strand)
     }
 )
 
 setMethod("nearest", c("GenomicRanges", "missing"),
-    function(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
+    function(x, subject, select=c("arbitrary", "all"),
+             algorithm=c("nclist", "intervaltree"), ignore.strand=FALSE)
     {
         select <- match.arg(select)
-        .nearest(x, x, select=select, ignore.strand=ignore.strand,
-                 ignoreSelf=TRUE)
+        .nearest(x, x, select=select, algorithm=match.arg(algorithm),
+                 ignore.strand=ignore.strand, ignoreSelf=TRUE)
     }
 )
 
@@ -339,17 +342,21 @@ setMethod("distance", c("GenomicRanges", "GenomicRanges"),
 ###
 
 setMethod("distanceToNearest", c("GenomicRanges", "GenomicRanges"),
-    function(x, subject, ignore.strand=FALSE, ...)
+    function(x, subject, algorithm=c("nclist", "intervaltree"),
+             ignore.strand=FALSE, ...)
     {
-        x_nearest <- nearest(x, subject, ignore.strand=ignore.strand, ...)
+        x_nearest <- nearest(x, subject, algorithm=match.arg(algorithm),
+                             ignore.strand=ignore.strand, ...)
         .distanceToNearest(x_nearest, x, subject, ignore.strand=ignore.strand)
     }
 )
 
 setMethod("distanceToNearest", c("GenomicRanges", "missing"),
-    function(x, subject, ignore.strand=FALSE, ...)
+    function(x, subject, algorithm=c("nclist", "intervaltree"),
+             ignore.strand=FALSE, ...)
     {
-        x_nearest <- nearest(x, ignore.strand=ignore.strand, ...)
+        x_nearest <- nearest(x, algorithm=match.arg(algorithm),
+                             ignore.strand=ignore.strand, ...)
         .distanceToNearest(x_nearest, x, x, ignore.strand=ignore.strand)
     }
 )
@@ -371,8 +378,8 @@ setMethod("distanceToNearest", c("GenomicRanges", "missing"),
              subjectLength=length(subject),
              distance=integer(0))
     } else {
-        distance = distance(x[queryHits], subject[subjectHits],
-                            ignore.strand=ignore.strand)
+        distance <- distance(x[queryHits], subject[subjectHits],
+                             ignore.strand=ignore.strand)
         Hits(queryHits, subjectHits, length(x), length(subject), distance)
     }
 }
diff --git a/man/nearest-methods.Rd b/man/nearest-methods.Rd
index f3564b9..bfd88d4 100644
--- a/man/nearest-methods.Rd
+++ b/man/nearest-methods.Rd
@@ -27,11 +27,15 @@
 \S4method{follow}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
 \S4method{follow}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
 
-\S4method{nearest}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
-\S4method{nearest}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"), ignore.strand=FALSE)
-
-\S4method{distanceToNearest}{GenomicRanges,GenomicRanges}(x, subject, ignore.strand=FALSE, ...)
-\S4method{distanceToNearest}{GenomicRanges,missing}(x, subject, ignore.strand=FALSE, ...)
+\S4method{nearest}{GenomicRanges,GenomicRanges}(x, subject, select=c("arbitrary", "all"),
+        algorithm=c("nclist", "intervaltree"), ignore.strand=FALSE)
+\S4method{nearest}{GenomicRanges,missing}(x, subject, select=c("arbitrary", "all"),
+        algorithm=c("nclist", "intervaltree"), ignore.strand=FALSE)
+
+\S4method{distanceToNearest}{GenomicRanges,GenomicRanges}(x, subject, algorithm=c("nclist", "intervaltree"),
+                  ignore.strand=FALSE, ...)
+\S4method{distanceToNearest}{GenomicRanges,missing}(x, subject, algorithm=c("nclist", "intervaltree"),
+                  ignore.strand=FALSE, ...)
 
 \S4method{distance}{GenomicRanges,GenomicRanges}(x, y, ignore.strand=FALSE, ...)
 }