diff --git a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java
index 1a277233..9822b2f7 100644
--- a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java
+++ b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/BEDtoGFFCLI.java
@@ -84,7 +84,7 @@ private String validateInput() throws IOException {
 	}
 
 	public static String getCLIcommand(File OUTPUT, File BED, boolean gzOutput) {
-		String command = "java -jar $SCRIPTMANAGER bed-manipulation bed-to-gff";
+		String command = "java -jar $SCRIPTMANAGER coordinate-manipulation bed-to-gff";
 		command += " " + BED.getAbsolutePath();
 		command += gzOutput ? " -z" : "";
 		command += " -o " + OUTPUT;
diff --git a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/ExpandBEDCLI.java b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/ExpandBEDCLI.java
index d08ff094..e06b92fe 100644
--- a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/ExpandBEDCLI.java
+++ b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/ExpandBEDCLI.java
@@ -121,7 +121,7 @@ private String validateInput() throws IOException {
 		return(r);
 	}
 	public static String getCLIcommand(File bedFile, File output, int size, boolean gzOutput, boolean byCenter) {
-		String command = "java -jar $SCRIPTMANAGER bed-manipulation expand-bed";
+		String command = "java -jar $SCRIPTMANAGER coordinate-manipulation expand-bed";
 		command += " " + bedFile.getAbsolutePath();
 		command += gzOutput ? " -z " : "";
 		command += " -o " + output.getAbsolutePath();
diff --git a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java
index a14eefce..93574310 100644
--- a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java
+++ b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/BED_Manipulation/SortBEDCLI.java
@@ -121,7 +121,7 @@ else if( center<0 ){
 	}
 
 	public static String getCLIcommand(File OUTPUT, File BED, File CDT, int startidx, int stopidx, boolean gzOutput) {
-		String command = "java -jar $SCRIPTMANAGER bed-manipulation sortBED";
+		String command = "java -jar $SCRIPTMANAGER coordinate-manipulation sort-bed";
 		command += " " + BED.getAbsolutePath();
 		command += " " + CDT.getAbsolutePath();
 		command += " -x " + startidx + " " + stopidx;
diff --git a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFCLI.java b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFCLI.java
index 83665880..61c8380c 100644
--- a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFCLI.java
+++ b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/ExpandGFFCLI.java
@@ -118,7 +118,7 @@ private String validateInput() throws IOException {
 		return(r);
 	}
 	public static String getCLIcommand(File bedFile, File output, int size, boolean byCenter) {
-		String command = "java -jar $SCRIPTMANAGER gff-manipulation expand-gff";
+		String command = "java -jar $SCRIPTMANAGER coordinate-manipulation expand-gff";
 		command += " " + bedFile.getAbsolutePath();
 		command += " -o " + output.getAbsolutePath();
 		command += byCenter ? " -c " + size : " -b " + size;
diff --git a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
index 88e475d0..4efe60cd 100644
--- a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
+++ b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
@@ -75,7 +75,7 @@ private String validateInput() throws IOException {
 		return(r);
 	}
 	public static String getCLIcommand(File GFF, File output) {
-		String command = "java -jar  $SCRIPTMANAGER gff-manipulation gff-to-bed";
+		String command = "java -jar  $SCRIPTMANAGER coordinate-manipulation gff-to-bed";
 		command += " " + GFF.getAbsolutePath();
 		command += " -o " + output.getAbsolutePath();
 		return command;
diff --git a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/SortGFFCLI.java b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/SortGFFCLI.java
index 9ca304ae..8ecf8401 100644
--- a/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/SortGFFCLI.java
+++ b/src/main/java/scriptmanager/cli/Coordinate_Manipulation/GFF_Manipulation/SortGFFCLI.java
@@ -122,7 +122,7 @@ else if( center<0 ){
 		return(r);
 	}
 	public static String getCLIcommand(File OUTPUT, File BED, File CDT, int startidx, int stopidx) {
-		String command = "java -jar $SCRIPTMANAGER gff-manipulation sortGFF";
+		String command = "java -jar $SCRIPTMANAGER coordinatesort-manipulation sort-gff";
 		command += " " + BED.getAbsolutePath();
 		command += " " + CDT.getAbsolutePath();
 		command += " -x " + startidx + " " + stopidx;