diff --git a/.gitignore b/.gitignore
index d356698..87df4e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 *.DS_store
 *~
+documentation/*
diff --git a/c++_implementation/Doxyfile b/c++_implementation/Doxyfile
index 834766a..006301f 100644
--- a/c++_implementation/Doxyfile
+++ b/c++_implementation/Doxyfile
@@ -1535,7 +1535,7 @@ FORMULA_TRANSPARENT    = YES
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
diff --git a/generateDocumentation.sh b/generateDocumentation.sh
new file mode 100755
index 0000000..d80047f
--- /dev/null
+++ b/generateDocumentation.sh
@@ -0,0 +1,32 @@
+#!/bin/bash
+
+#script to generate documentation
+
+rm -rf documentation/* 
+rmdir documentation 
+mkdir documentation
+cd matlab_implementation
+rm -rf Doc/*
+rmdir Doc
+doxygen Doxyfile
+mv Doc/html ../documentation/matlab
+mkdir ../documentation/matlab/assets
+mkdir -p ../documentation/matlab/assets/continuous_discrete/examples
+cp continuous_discrete/examples/*.png ../documentation/matlab/assets/continuous_discrete/examples # 2>/dev/null
+mkdir -p ../documentation/matlab/assets/cubature/examples
+cp cubature/examples/*.png ../documentation/matlab/assets/cubature/examples #2>/dev/null
+mkdir -p ../documentation/matlab/assets/discrete_discrete/examples
+cp discrete_discrete/examples/*.png ../documentation/matlab/assets/discrete_discrete/examples #2>/dev/null
+mkdir -p ../documentation/matlab/assets/ensemble_stochastic/examples
+cp ensemble_stochastic/examples/*.png ../documentation/matlab/assets/ensemble_stochastic/examples #2>/dev/null
+mkdir -p ../documentation/matlab/assets/particle/examples
+cp particle/examples/*.png ../documentation/matlab/assets/particle/examples #2>/dev/null
+cd ..
+
+cd c++_implementation
+rm -rf Doc/*
+rmdir Doc
+doxygen Doxyfile
+mv html ../documentation/cpp
+cp assets/*.png ../documentation/cpp
+cd ..