diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index 5ca7ea7ba675c757b7c033c76e1601162d196c0a..acb346c4eb79db66566bf59b411849832a9fb3d3 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -35,8 +35,13 @@ class AriaEcContactMap(object):
         logger.debug("Args:\n" + json.dumps(self.settings.contactmap.args,
                                             indent=4))
         # ----------------------------- Input -------------------------------- #
-        self.outprefix = get_filename(self.settings.contactmap.args.get(
-            "seq", None)) + self.settings.contactmap.args.get("prefix", "")
+        if self.settings.contactmap.args.get("prefix"):
+            self.outprefix = "_".join((get_filename(
+                self.settings.contactmap.args.get("seq", None)),
+                self.settings.contactmap.args.get("prefix", "")))
+        else:
+            self.outprefix = get_filename(
+                self.settings.contactmap.args.get("seq", None))
         # Load Sequence file
         self.protein.set_aa_sequence(self.settings.contactmap.args.get("seq", None))
         # Load secondary structure prediction file
diff --git a/setup.py b/setup.py
index 7dcdd102a677ab905220a73bcbe544e84d7caa99..21ec913661f41066a931362b86acd1e7bfe6fe75 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,23 @@
 import os
+import subprocess
 from setuptools import setup, find_packages, Command
 
-__version_info__ = (0, 0, 0)    # MAJOR, MINOR, PATCH
+# Fetch version from git tags, and write to version.py.
+# Also, when git is not available (PyPi package), use stored version.py.
+version_py = os.path.join(os.path.dirname(__file__), 'version.py')
+try:
+    version_git = subprocess.check_output(["git", "describe",
+                                           "--tags"]).rstrip()
+except subprocess.CalledProcessError:
+    with open(version_py, 'r') as fh:
+        version_git = open(version_py).read().strip().split('=')[-1].replace('"',
+                                                                             '')
+
+version_msg = "# Do not edit this file, pipeline versioning is governed by git tags"
+with open(version_py, 'w') as pyv:
+    pyv.write(version_msg + os.linesep + "__version__=" + version_git)
+
+__version_info__ = (0, 1, 0)    # MAJOR, MINOR, PATCH
 __version__ = '.'.join((str(i) for i in __version_info__))
 
 
@@ -15,7 +31,8 @@ class CleanCommand(Command):
     def finalize_options(self):
         pass
 
-    def run(self):
+    @staticmethod
+    def run():
         os.system('rm -vrf ./build ./dist ./*.pyc ./*.tgz ./*.egg '
                   './*.egg-info')
 
@@ -28,7 +45,7 @@ with open('README.rst') as f:
 
 setup(
     name="ariaec",
-    version=__version__,
+    version="{ver}".format(ver=version_git),
     packages=find_packages(),
 
     scripts=['bin/ec2aria.py'],