diff --git a/sdg-cli/src/main/java/es/upv/mist/slicing/cli/Slicer.java b/sdg-cli/src/main/java/es/upv/mist/slicing/cli/Slicer.java
index cc34c1c5fd9fba2c82aae5946cda10feb2df8368..460161a1ae61950a05618dfb28e765e00a3e7dcc 100644
--- a/sdg-cli/src/main/java/es/upv/mist/slicing/cli/Slicer.java
+++ b/sdg-cli/src/main/java/es/upv/mist/slicing/cli/Slicer.java
@@ -13,6 +13,7 @@ import es.upv.mist.slicing.graphs.sdg.SDG;
 import es.upv.mist.slicing.slicing.FileLineSlicingCriterion;
 import es.upv.mist.slicing.slicing.Slice;
 import es.upv.mist.slicing.slicing.SlicingCriterion;
+import es.upv.mist.slicing.utils.NodeHashSet;
 import es.upv.mist.slicing.utils.StaticTypeSolver;
 import org.apache.commons.cli.*;
 
@@ -22,6 +23,7 @@ import java.io.PrintWriter;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.util.stream.Stream;
 
 public class Slicer {
     protected static final String HELP_HEADER = "Java SDG Slicer: extract a slice from a Java program. At least" +
@@ -215,13 +217,16 @@ public class Slicer {
         StaticJavaParser.getConfiguration().setAttributeComments(false);
 
         // Build the SDG
-        NodeList<CompilationUnit> units = new NodeList<>();
+        Set<CompilationUnit> units = new NodeHashSet<>();
         try {
-            for (File directory : dirIncludeSet)
-                units.add(StaticJavaParser.parse(directory));
-            CompilationUnit scUnit = StaticJavaParser.parse(scFile);
-            if (!units.contains(scUnit))
-                units.add(scUnit);
+            for (File file : dirIncludeSet) {
+                if (file.isDirectory())
+                    for (File f : (Iterable<File>) findAllJavaFiles(file)::iterator)
+                        units.add(StaticJavaParser.parse(f));
+                else
+                    units.add(StaticJavaParser.parse(file));
+            }
+            units.add(StaticJavaParser.parse(scFile));
         } catch (FileNotFoundException e) {
             throw new ParseException(e.getMessage());
         }
@@ -235,7 +240,7 @@ public class Slicer {
             default:
                 throw new IllegalArgumentException("Unknown type of graph. Available graphs are SDG, ASDG, PSDG, ESSDG");
         }
-        sdg.build(units);
+        sdg.build(new NodeList<>(units));
 
         // Slice the SDG
         SlicingCriterion sc = new FileLineSlicingCriterion(scFile, scLine);
@@ -258,6 +263,24 @@ public class Slicer {
         }
     }
 
+    protected Stream<File> findAllJavaFiles(File directory) {
+        Stream.Builder<File> builder = Stream.builder();
+        findAllJavaFiles(directory, builder);
+        return builder.build();
+    }
+
+    protected void findAllJavaFiles(File directory, Stream.Builder<File> builder) {
+        File[] files = directory.listFiles();
+        if (files == null)
+            return;
+        for (File f : files) {
+            if (f.isDirectory())
+                findAllJavaFiles(f, builder);
+            else if (f.getName().endsWith(".java"))
+                builder.add(f);
+        }
+    }
+
     protected String getDisclaimer(CompilationUnit.Storage s) {
         return String.format("\n\tThis file was automatically generated as part of a slice with criterion" +
                         "\n\tfile: %s, line: %d, variable(s): %s\n\tOriginal file: %s\n",
diff --git a/sdg-core/src/main/java/es/upv/mist/slicing/graphs/CallGraph.java b/sdg-core/src/main/java/es/upv/mist/slicing/graphs/CallGraph.java
index d6a2e6b310c6f9f6d8b80349f908747fb2056b29..f0cdb2ce4ebc7cbb1402921f31ecac0af74342a6 100644
--- a/sdg-core/src/main/java/es/upv/mist/slicing/graphs/CallGraph.java
+++ b/sdg-core/src/main/java/es/upv/mist/slicing/graphs/CallGraph.java
@@ -40,7 +40,6 @@ import java.util.stream.Stream;
  */
 public class CallGraph extends DirectedPseudograph<CallGraph.Vertex, CallGraph.Edge<?>> implements Buildable<NodeList<CompilationUnit>> {
     private final Map<CallableDeclaration<?>, CFG> cfgMap;
-    private final Map<CallableDeclaration<?>, Vertex> vertexDeclarationMap = ASTUtils.newIdentityHashMap();
     private final ClassGraph classGraph;
 
     private boolean built = false;
@@ -116,27 +115,21 @@ public class CallGraph extends DirectedPseudograph<CallGraph.Vertex, CallGraph.E
         arg.accept(new VoidVisitorAdapter<Void>() {
             @Override
             public void visit(MethodDeclaration n, Void arg) {
-                addDeclaration(n);
+                addVertex(new Vertex(n));
                 super.visit(n, arg);
             }
 
             @Override
             public void visit(ConstructorDeclaration n, Void arg) {
-                addDeclaration(n);
+                addVertex(new Vertex(n));
                 super.visit(n, arg);
             }
         }, null);
     }
 
-    protected void addDeclaration(CallableDeclaration<?> n) {
-        Vertex v = new Vertex(n);
-        vertexDeclarationMap.put(n, v);
-        addVertex(v);
-    }
-
     protected boolean addEdge(CallableDeclaration<?> source, CallableDeclaration<?> target, Resolvable<? extends ResolvedMethodLikeDeclaration> call) {
         Edge<?> edge = new Edge<>(call, findGraphNode(call, source));
-        return addEdge(vertexDeclarationMap.get(source), vertexDeclarationMap.get(target), edge);
+        return addEdge(findVertexByDeclaration(source), findVertexByDeclaration(target), edge);
     }
 
     /** Find the calls to methods and constructors (edges) in the given list of compilation units. */