diff --git a/panphlan_map.py b/panphlan/panphlan_map.py
similarity index 99%
rename from panphlan_map.py
rename to panphlan/panphlan_map.py
index 4cc0439..5758b21 100755
--- a/panphlan_map.py
+++ b/panphlan/panphlan_map.py
@@ -17,7 +17,7 @@
 from argparse import ArgumentParser
 from collections import defaultdict
 from shutil import copyfileobj
-from utils import end_program, show_interruption_message, show_error_message, time_message, find
+from .utils import end_program, show_interruption_message, show_error_message, time_message, find
 import bz2, fnmatch, multiprocessing, operator, os, subprocess, sys, tempfile, time
 from distutils.version import LooseVersion
 
diff --git a/panphlan_new_pangenome_generation.py b/panphlan/panphlan_new_pangenome_generation.py
similarity index 100%
rename from panphlan_new_pangenome_generation.py
rename to panphlan/panphlan_new_pangenome_generation.py
diff --git a/panphlan_pangenome_generation.py b/panphlan/panphlan_pangenome_generation.py
similarity index 100%
rename from panphlan_pangenome_generation.py
rename to panphlan/panphlan_pangenome_generation.py
diff --git a/panphlan_profile.py b/panphlan/panphlan_profile.py
similarity index 99%
rename from panphlan_profile.py
rename to panphlan/panphlan_profile.py
index 214cb9f..0dc61d4 100755
--- a/panphlan_profile.py
+++ b/panphlan/panphlan_profile.py
@@ -19,7 +19,7 @@
 from argparse import ArgumentParser
 from collections import defaultdict
 from random import randint
-from utils import end_program, show_interruption_message, show_error_message, time_message, find
+from .utils import end_program, show_interruption_message, show_error_message, time_message, find
 import fnmatch, operator, os, subprocess, sys, time
 import bz2
 
diff --git a/tools/RNAseq_get_non_coding_reads.sh b/panphlan/tools/RNAseq_get_non_coding_reads.sh
similarity index 100%
rename from tools/RNAseq_get_non_coding_reads.sh
rename to panphlan/tools/RNAseq_get_non_coding_reads.sh
diff --git a/tools/download_all_databases.sh b/panphlan/tools/download_all_databases.sh
similarity index 100%
rename from tools/download_all_databases.sh
rename to panphlan/tools/download_all_databases.sh
diff --git a/tools/roary2panphlan.py b/panphlan/tools/roary2panphlan.py
similarity index 100%
rename from tools/roary2panphlan.py
rename to panphlan/tools/roary2panphlan.py
diff --git a/utils.py b/panphlan/utils.py
similarity index 100%
rename from utils.py
rename to panphlan/utils.py
diff --git a/setup.py b/setup.py
index dfd81b6..304640a 100644
--- a/setup.py
+++ b/setup.py
@@ -10,11 +10,14 @@
     author='Matthias Scholz',
     author_email='matthias.scholz.de@gmail.com',
     url='http://github.com/SegataLab/panphlan/',
-    py_modules=['panphlan_map', 'panphlan_profile', 'panphlan_new_pangenome_generation', 'panphlan_pangenome_generation', 'utils'],
-    entry_points = { "console_scripts" : [ "panphlan_map = panphlan_map:main",
-                                           "panphlan_profile = panphlan_profile:main",
-                                           "panphlan_new_pangenome_generation = panphlan_new_pangenome_generation:main",
-                                           "panphlan_pangenome_generation = panphlan_pangenome_generation:main"
+    packages=setuptools.find_namespace_packages(),
+    package_data = { 'panphlan' : [
+        'panphlan/tools/*'
+    ]},
+    entry_points = { "console_scripts" : [ "panphlan_map.py = panphlan.panphlan_map:main",
+                                           "panphlan_profile.py = panphlan.panphlan_profile:main",
+                                           "panphlan_new_pangenome_generation.py = panphlan.panphlan_new_pangenome_generation:main",
+                                           "panphlan_pangenome_generation.py = panphlan.panphlan_pangenome_generation:main"
                                          ] },
     long_description_content_type='text/markdown',
     long_description=open('README.md').read(),