diff --git a/doc/developer.texinfo b/doc/developer.texinfo
index 0951936384..52bbd5591a 100644
--- a/doc/developer.texinfo
+++ b/doc/developer.texinfo
@@ -259,7 +259,7 @@ call the new invariant's @code{get_proto} method and recompile Daikon.
 @item
 If you do not wish to edit the Daikon source code, then compile the new
 invariant and put its @file{.class} file on your classpath.  Then, invoke
-Daikon with the @option{--user_defined_invariant} command-line argument
+Daikon with the @option{--user-defined-invariant} command-line argument
 (@pxref{Options to control invariant detection,,,daikon,Daikon User Manual}).
 @end itemize
 
diff --git a/java/daikon/Daikon.java b/java/daikon/Daikon.java
index 1e7c1e1b73..0bc7004741 100644
--- a/java/daikon/Daikon.java
+++ b/java/daikon/Daikon.java
@@ -1498,7 +1498,7 @@ public static String getOptarg(Getopt g) {
   }
 
   /**
-   * Invariants passed on the command line with the {@code --user_defined_invariant} option. A list
+   * Invariants passed on the command line with the {@code --user-defined-invariant} option. A list
    * of class names in the format required by {@link Class#forName(String)}.
    */
   private static List<@ClassGetName String> userDefinedInvariants =
diff --git a/scripts/runcluster.pl b/scripts/runcluster.pl
index bf31f6de12..1eddca1ba8 100755
--- a/scripts/runcluster.pl
+++ b/scripts/runcluster.pl
@@ -209,7 +209,7 @@ ()
 }
 
 my $invfile = "runcluster_temp_$algorithm-$ncluster.inv";
-$command = "java -cp $SCRIPTDIR/../daikon.jar -Xmx7g daikon.Daikon -o $invfile --config_option daikon.PptTopLevel.pairwise_implications=true --var_omit_pattern=\"class\" --no_text_output --no_show_progress $spinfo_file $decls_new " . join(' ', @new_dtraces) . " 2>&1 > runcluster_temp_Daikon_output.txt";
+$command = "java -cp $SCRIPTDIR/../daikon.jar -Xmx7g daikon.Daikon -o $invfile --config_option daikon.PptTopLevel.pairwise_implications=true --var-omit-pattern=\"class\" --no_text_output --no_show_progress $spinfo_file $decls_new " . join(' ', @new_dtraces) . " > runcluster_temp_Daikon_output.txt 2>&1";
 system_or_die($command, $verbose);
 
 $invfile =~ /(.*)\.inv/;
diff --git a/scripts/trace-purge-vars.pl b/scripts/trace-purge-vars.pl
index f3b95d73d9..c75fdc9a7e 100755
--- a/scripts/trace-purge-vars.pl
+++ b/scripts/trace-purge-vars.pl
@@ -8,7 +8,7 @@
 # regular expression.  (Its name is taken from grep.)
 
 # This script reduces the size of a trace file, but typically, using
-# Daikon's --var_omit_pattern flag is a better option.
+# Daikon's --var-omit-pattern flag is a better option.
 
 # I'm intentionally not operating by paragraphs, because I want the regexp
 # to only apply to the variable lines.
diff --git a/tests/daikon-tests/RatPoly/Makefile b/tests/daikon-tests/RatPoly/Makefile
index 251dee351f..a8c885bd79 100644
--- a/tests/daikon-tests/RatPoly/Makefile
+++ b/tests/daikon-tests/RatPoly/Makefile
@@ -13,7 +13,7 @@ ESC_ON:=1
 
 include ../../Makefile.common
 
-# USER_DAIKON_OPTIONS:=--var_omit_pattern=".*wrapped.*"
+# USER_DAIKON_OPTIONS:=--var-omit-pattern=".*wrapped.*"
 
 # USER_DAIKON_OPTIONS:=--ppt-select-pattern="^Rat" --config config.txt